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WO2016149710A2 - Anticorps neutralisant le vih-1 et leurs utilisations - Google Patents

Anticorps neutralisant le vih-1 et leurs utilisations Download PDF

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Publication number
WO2016149710A2
WO2016149710A2 PCT/US2016/023488 US2016023488W WO2016149710A2 WO 2016149710 A2 WO2016149710 A2 WO 2016149710A2 US 2016023488 W US2016023488 W US 2016023488W WO 2016149710 A2 WO2016149710 A2 WO 2016149710A2
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WIPO (PCT)
Prior art keywords
antibody
antibodies
hiv
chain
mper
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PCT/US2016/023488
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English (en)
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WO2016149710A8 (fr
WO2016149710A3 (fr
Inventor
Barton F. Haynes
Hua-Xin Liao
M. Anthony Moody
Latonya WILLIAMS
Kevin J. WIEHE
Gilad Adi OFEK
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Duke University
University Of Maryland, College Park
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Application filed by Duke University, University Of Maryland, College Park filed Critical Duke University
Priority to CA2979708A priority Critical patent/CA2979708A1/fr
Priority to US15/559,314 priority patent/US11071783B2/en
Priority to AU2016232693A priority patent/AU2016232693B2/en
Priority to EP16765900.2A priority patent/EP3271022A4/fr
Publication of WO2016149710A2 publication Critical patent/WO2016149710A2/fr
Publication of WO2016149710A3 publication Critical patent/WO2016149710A3/fr
Publication of WO2016149710A8 publication Critical patent/WO2016149710A8/fr
Priority to US17/357,725 priority patent/US11944681B2/en

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
    • A61K39/42—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum viral
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
    • A61K39/44—Antibodies bound to carriers
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • A61P31/18—Antivirals for RNA viruses for HIV
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C07K16/1036—Retroviridae, e.g. leukemia viruses
    • C07K16/1045—Lentiviridae, e.g. HIV, FIV, SIV
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A61K2039/507—Comprising a combination of two or more separate antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2299/00—Coordinates from 3D structures of peptides, e.g. proteins or enzymes
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/24—Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/54—F(ab')2
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/55—Fab or Fab'
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

  • the invention relates to the identification of monoclonal HIV-1 neutralizing antibodies, such as, but not limited to, antibodies that bind to the membrane-proximal region of HIV-1 gp41, their recombinant expression and purification and uses.
  • mAbs neutralizing monoclonal antibodies
  • gp41 bnAbs broadly neutralizing antibodies
  • MPER membrane-proximal region
  • the invention provides an antibody or fragment thereof with the binding specificity of an MPER antibody as described herein.
  • the MPER antibody from Figure 13, Figure 55, Figure 56 or Figures 30-33 (antibodies with mutations in the DH512 or DH511 VH chain).
  • combination mutations in the DH512 or DH511 VHCDR3 could include VH LlOOdF together with TlOOaW Figures 31 and 32); VH_L100dW together with TlOOaW ( Figures 31 and 32).
  • Non-limiting examples include antibodies comprising VH or VL chains from DH511, DH512, DH512 K3, DH512-L100dF, DH513, DH514, DH515, DH516, DH517, DH518, lineage members.
  • the antibody or fragment thereof is fully human and recombinantly produced.
  • some of the VH and/VL chains are isolated from human subject who have been naturally infected with HIV.
  • the antibody is not naturally occurring.
  • the antibody comprises naturally occurring pair of VH and VL chains.
  • the antibody comprises naturally occurring pair of VH and VL chains wherein the Fc portion of the antibody is not the natural isotype or portion of the naturally occurring pair of VH and VL chains.
  • the antibody is computationally designed, for example based on some naturally isolated VH and VL sequences.
  • the antibody is computationally designed, e.g., UCA, Intermediates in the antibody lineages.
  • the antibody comprises a non-naturally occurring pairing of VH and VL chains, wherein the VH or VL individually could be isolated from a subject.
  • the antibody comprises VH chain or HCDRs of a VH chain of one clonal member, and VL or LCDRs of another clonal member, i.e., a non-naturally occurring antibody comprising sequences derived from natural pairs.
  • the antibody or fragment thereof comprises a VH chain that is 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the VH chain of antibody DH511, DH512, DH513, DH514, DH515, DH516, DH517, DH518, DH536, DH537, DH491 or DH493, or an antibody from Example 10, 11 or 12.
  • the antibody or fragment thereof comprises a VL chain that is 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the VL chain of antibody DH511, DH512, DH513, DH514, DH515, DH516, DH517, DH518, DH536, DH537, DH491 or DH493, or an antibody from Example 10, 11 or 12.
  • the antibody or fragment thereof comprises a VH chain that is 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the VH chain of antibody DH511, DH512, DH513, DH514, DH515, DH516, DH517, DH518, DH536, DH537, DH491 or DH493 and further comprises a VL chain that is 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the VL chain of antibody DH511, DH512, DH513, DH514, DH515, DH516, DH517, DH518, DH536, DH537, DH491 or DH493, or an antibody from Example 10, 11 or 12.
  • the antibody or fragment thereof comprises a VH which comprises the HCDR1, HCDR2, and HCDR3 of antibody DH511, DH512, DH513, DH514, DH515, DH516, DH517, DH518, DH536, DH537, DH491 or DH493, or an antibody from Example 10, 11 or 12.
  • the antibody or fragment thereof comprises a VL which comprises the LCDR1, LCDR2, and LCDR3 of antibody DH511, DH512, DH513, DH514, DH515, DH516, DH517, DH518, DH536, DH537, DH491 or DH493, or an antibody from Example 10, 11 or 12.
  • the antibody or fragment thereof comprises a VH which comprises the HCDR1, HCDR2, and HCDR3 of antibody DH511, DH512, DH513, DH514, DH515, DH516, DH517, DH518, DH536, DH537, DH491 or DH493, or an antibody from Example 10, 11 or 12 and further comprises the complementary VL which comprises the LCDR1, LCDR2, LCDR3 of antibody DH511, DH512, DH513, DH514, DH515, DH516, DH517, DH518, DH536, DH537, DH491 or DH493, or an antibody from Example 10, 11 or 12.
  • the antibody or fragment thereof comprises VH and VL of antibody DH511, DH512, DH513, DH514, DH515, DH516, DH517, DH518, DH536,
  • DH537 DH491 or DH493, or an antibody from Example 10, 11 or 12.
  • the antibody is DH511, DH512, DH513, DH514, DH515,
  • the invention provides a pharmaceutical composition comprising anyone of the antibodies of the invention or fragments thereof or any combination thereof.
  • the invention provides a pharmaceutical composition comprising anyone of the antibodies of the invention, or a combination thereof.
  • the composition comprises an antibody or a fragment thereof which is recombinantly produced in CHO cells.
  • the invention provides a pharmaceutical composition comprising a vector comprising a nucleic acid encoding anyone of inventive antibodies or fragments.
  • the nucleic acids are optimized for expression in human host cells.
  • the vector is suitable for gene delivery and expression.
  • Non-limiting examples of such vectors include adenoviral vectors (Ads), adeno associated virus based vectors (AAVs), or a combination thereof.
  • compositions further comprise an antibody or a fragment thereof comprising the VH and VL chains of antibody DH540.
  • compositions further comprise an antibody or a fragment thereof comprising VH and VL chain of antibody CH557 or DH270 lineage antibody, for example without limitation DH542, DH542-QSA, DH542 L4..
  • the invention provides a bispecific antibody which comprises gp41
  • the MPER binding portion of the bispecific antibody comprises VH and/or VL chains, variants or fragments thereof.
  • the invention provides methods to treat or prevent HIV-1 infection in a subject comprising administering to the subject the pharmaceutical composition of any one of the preceding claims in a therapeutically effective amount.
  • the pharmaceutical composition is administered in a therapeutically effective regimen.
  • Figure 1 shows Neutralization-based Epitope Prediction (NEP) Analysis.
  • Neutralization-based epitope prediction analysis The predicted relevant prevalence of antibody clusters [(10 epitopes targeting sites of vulnerability (CD4 binding site, V1/V2, MPER, glycan V3)] is shown as a heat map, with dark color intensity (higher fractional number) corresponding to a stronger neutralization signal. Plasma neutralization breadth is shown, and numbers in each row add up to 1.00. NEP algorithm reference: [Georgiev IS et al Science 340: 751-756].
  • FIG. 2 shows MPR.03 Hook sequence (SEQ ID NOs: 1-2).
  • MPR.03 is a biotinylated peptide containing lysines at both ends for solubility
  • KKKNEQELLELDKWASLWNWFDITNWLWYIRKKK-biotin (SEQ ID NO: 463) used to pull out gp41 antibodies from blood memory B cell sorts See Morris L. et al. (2011) PLoS ONE 6(9): e23532.
  • FIG 3 shows a representative CH0210 mper03 sort (sort #1).
  • FIG. 4 shows V(D)J Rearrangement of MPER Antibodies Isolated from Four HIV-1 Infected Individuals. * indicates that these mAbs neutralized the tier 1 isolate MN in TZM-bl cells. Mutation refers to VH nucleotide sequence somatic mutation percentages in the variable heavy (VH) immunoglobulin (Ig) genes.
  • VH variable heavy
  • Ig immunoglobulin
  • Figure 5 shows Neutralization Titers of MPER Antibodies Isolated from Four HIV-1 Infected Individuals using a small panel of HIV-1 isolates in the TZMbl pseudovirus inhibition assay.
  • Figure 6 shows the MPER BnAb DH511 VH Phylogram of the B Cell Clonal Lineage Derived from Subject 0210.
  • Antibodies in clone DH511 include the following: DH511, DH512, DH513, DH514, DH515, DH516 and DH520.
  • Figure 7 shows summary results of neutralization of gp41 antibodies against a panel of 30 HIV-1 tier 2 isolates in the TZMbl pseudovirus neutralization assay. Data show that antibodies in the DH511 B cell clonal lineage (DH511-DH516) all neutralize 100% of 30
  • HIV-1 isolates tested in the TZMbl Env pseudovirus neutralization assay tested in the TZMbl Env pseudovirus neutralization assay.
  • Figure 8 shows Neutralizing Breadth and Potency of DH512, DH517 and DH518
  • DH512 neutralizes 100% of HIV strains and is as at least as potent as 10E8.
  • Figure 9 shows Neutralizing Breadth and Potency of various HIV-1 BnAbs that are candidates for being combined with DH512 or other antibodies in Figure 4 for a potent mixture of bnAbs.
  • DH270IA1 is II in the DH270 lineage (See Figure 26, and US Ser. No. 62/056,568 filed September 28, 214)
  • Figure 10 shows Neutralizing Breadth and Potency of some candidate bnAbs for single or combination use.
  • Figure 11 shows summary of Clone DH511 binding to the indicated peptides (SEQ ID NOs: 3-14) in ELISA.
  • Clone DH511 antibodies bind at the C-terminus of the MPER.
  • + indicates that antibodies in the Clone DH511 bind to the peptide.
  • the summary shows that DH511 clone antibodies do not bind the peptides when D674 is mutated to S674.
  • the twelve sequences of the peptides (without the three lysines at the N- and C- end) are shown in SEQ
  • antibody DH511 requires an aspartic acid at amino acid position 674 for binding.
  • Figure 12 shows nucleic acid sequences of antibodies DH511-518, DH536 and 537 (SEQ ID Nos: 15 to 34).
  • Figure 13 shows amino acid sequences of antibodies DH511-518, DH536 and 537. (SEQ ID Nos: 35 to 55)
  • Figures 14A-B show Alignment of VH (Fig. 14A; (SEQ ID Nos: 56-61)) and VL (Fig. 14B (SEQ ID Nos: 62-67)) Sequences of BnAb DH511 Clonal Lineage.
  • Bolded is the sequence of CDR1
  • underlined is the sequence of CDR2
  • italicized is the sequence of CDR3 of the DH511 VH chain and DH511 VL chain.
  • the CDRs of the VH and VL sequences of the other antibodies DH512, DH513, DH514, DH515, and DH516 can be readily determined based on the sequence alignment.
  • Figures 15A-B show Alignment of VH (Fig. 15A (SEQ ID Nos: 68-76)) and VL (Fig. 15B (SEQ ID Nos: 77-85)) sequences of MPER BnAbs.
  • Bolded is the sequence of CDR1
  • italicized is the sequence of CDR2
  • underlined is the sequence of CDR3 of VH or VL of the listed MPER antibodies.
  • Figure 16 shows sequences of MPER alanine mutants (SEQ ID NOs: 86-112) screened in ELISA. All antibodies in the DH51 clone showed weak binding to this peptide set. DH517 (Ab510053) strongly bound to MPER656 peptide and showed decreased binding to several residues (A4, A6-A13, A16-A18, A20, A23, A24, A26) using the ala substituted peptides in table.
  • Figure 17 shows Binding of DH517 (Ab510053) to alanine substituted MPER-26 peptides. The binding studies do not conclusively map the DH517epitope.
  • Figure 18 shows MPER656 variants (SEQ ID NOs: 13-124) screened in ELISA. Residues shown in light blue (underlined) indicate positions that differ from MPER656- biotin.
  • Figure 19 shows Binding of DH511 (Ab510056) to MPER656 variants
  • Figure 20 shows Binding of DH512 (Ab510049) to MPER656 variants
  • Figure 21 shows Binding of DH513 (Ab570022) to MPER656 variants
  • Figure 22 shows Binding of DH514 (Ab570029) to MPER656 variants
  • Figure 23 shows Binding of DH515 (Ab510052) to MPER656 variants
  • Figure 24 shows Binding of DH516 (Ab510048) to MPER656 variants
  • Figure 25 shows Binding of DH518 (Ab570010) to MPER656 variants.
  • Figure 26 shows the amino acids sequences of VH (SEQ ID NOs: 137-148) and VL
  • SEQ ID NOs: 161-172 chains of antibodies of the DH270 lineage, and nucleic acid sequences (SEQ ID NOs: 125-136 (VH); SEQ ID NOs: 149-160 (VL)) encoding these amino acids. CDRs are highlighted and underlined in the UCA.
  • Figure 27A shows amino acid (SEQ ID Nos: 173 and 174) and nucleic acid sequences (SEQ ID Nos: 175 and 176) of CD4bs antibody CH557.
  • Figure 27B shows amino acid sequences of VH chains of antibodies from CH235 lineage (SEQ ID NOs: 177-188).
  • Figure 27C shows amino acid sequences of VL chains of antibodies from CH235 lineage (SEQ ID NOs: 189-198).
  • Figure 28 A shows neutralization Breadth and Potency of Plasma and Memory B cell (MBC)-derived MPER bnAbs.
  • Figure 29A and B show neutralization data from TZM-bl assay (Titer in TZM.bl cells (ug/ml) for DH512 K3 and other chimeric antibodies compared to DH512 and 10E8.
  • the data in the first column is historic data when DH512 was run in this panel previously.
  • DH512 was run at the same time as DH512 K3 but is listed as Ab510049 in this assay;
  • Figure 30 shows positions in the VHCDR3 chain of DH511 which could be mutated. Amino acid positions refer to Kabat numbering. Most mutations are to changes to W, but F, L or possibly other substitutions can be tried.
  • Figure 31 shows positions in the VHCDR3 chain of DH512 which could be mutated. Amino acid positions refer to Kabat numbering for the DH512VH chain:
  • Figure 32 shows positions outside of VHCDR3 which could be mutated. Most mutations are to changes to W, but F, L or possibly other substitutions can also be tried.
  • Figure 33 shows amino acid sequences (SEQ ID NOs: 199-216) of some of the DH512 mutants from Figure 31.
  • FIG. 34 shows neutralization data for a set of 16 mutations from Figure 31.
  • DH512 is referred to as DH512 (Ab510049_4A): its heavy chain is H510049 4 and its light chain is K510032
  • Figure 35 shows summary of anti-cardiolipin activity of various antibodies as measured by QUANTA Lite® ACA IgG III kit. Data plotted are representative of 2 independent experiments. mAb were run in duplicate in the second assay. Mean error and standard deviation are shown. Data were consistent between assays. Dotted line indicates positivity cut-off of 0.18. mAbs with OD values above 0.18 are bolded in the figure legend (DH514, DH518-315 HC, DH51 l-I6-4a through DH511 I1 4A; 4E10).
  • Figure 36 shows a summary of self-reactivity data of MPER antibodies.
  • Figure 37 shows summary results of neutralization data of DH512 and 10E8 against a panel of HIV-1 isolates in the TZMbl pseudovirus neutralization assay. Values represent IC50 in ⁇ g/ml. Figure 37 also shows the mean IC50 and percent of isolates neutralized at different IC50 values.
  • Figure 38 shows summary results of neutralization data of DH512 and 10E8 against a panel of HIV-1 isolates in the TZMbl pseudovirus neutralization assay. Values represent IC80 in ⁇ g/ml. Figure 38 also shows the mean IC80 and percent of isolates neutralized at different IC80 values.
  • FIG 39 shows Experimental Overview of Paired VH-VL Sequencing and antibody identification (Example 10).
  • V gene repertoire sequencing Identification of individual monoclonal antibodies requires the generation of a sample-specific database of IgG VH sequences constructed by next-generation sequencing of mature B cells isolated from the PBMCs of the donor. Reads are processed bioinformatically to obtain a database of unique VH sequences, which then are clustered into clonotypes according to their CDR3 sequences. The obtained database is used to interpret the MS spectra.
  • F(ab)2 purification and proteomic analysis F(ab)2 fragments are prepared from total serum IgG and subjected to antigen- affinity chromatography (monomelic gpl20).
  • Proteins in the elution and flow-through are denatured and reduced, alkylated, trypsin-digested and analyzed by high resolution LC- MS/MS. Spectra are interpreted with the sample-specific VH database and peptides uniquely associated with a single CDR3 are used to identify full-length VH sequences.
  • Figure 40 shows MPER BnAb DH511 Clonal Lineage Derived from African
  • Figure 41 shows Neutralization Activity (IC50) of MPER Antibodies Identified by Paired VH:VL Sequencing Technology (Example 10). Summary data of two independent assays.
  • Figure 42 shows Neutralization Activity (IC80) of MPER Antibodies Identified by Paired VH:VL Sequencing Technology (Example 10). Summary data of two independent assays.
  • Figure 43 shows Nucleotide Alignment of MPER Antibody Heavy Chain Sequences (SEQ ID NOs: 217-229).
  • Figure 44 shows Amino Acid Alignment of MPER Antibody Heavy Chain Sequences (SEQ ID NOs: 230-242).
  • Figure 45 shows Nucleotide Alignment of MPER Antibody Light Chain Sequences (SEQ ID NOs: 243-252).
  • Figure 46 shows Amino Acid Alignment of MPER Antibody Light Chain Sequences (SEQ ID NOs: 253-262).
  • Figure 47 shows Immunogenetic Characteristics of MPER Antibodies - Original Pairings.
  • Figures 48 shows epitope mapping of antibodies of Example 10. Binding to various MPER peptides in an ELISA assay was used to map the epitopes of these MPER antibodies.
  • Figures 49 show epitope mapping of antibodies of Example 10. Binding to various MPER peptides in an ELISA assay was used to map the epitopes of these MPER antibodies.
  • Figures 50 show epitope mapping of antibodies of Example 10. Binding to various MPER peptides in an ELISA assay was used to map the epitopes of these MPER antibodies.
  • Figures 51 show epitope mapping of antibodies of Example 10. Binding to various MPER peptides in an ELISA assay was used to map the epitopes of these MPER antibodies.
  • Figures 52 show epitope mapping of antibodies of Example 10. Binding to various MPER peptides in an ELISA assay was used to map the epitopes of these MPER antibodies.
  • Figure 53 shows Poly/Autoreactivity analysis of DH51 l_5a.
  • Antibody DH51 l_5a appears to be autoreactive with one protein (NUDC).
  • Figure 54 shows Poly/Autoreactivity analysis of DH51 l_5b. Antibody DH51 l_5b appears to be polyreactive.
  • Figure 55 shows Antibody Pairings - Heavy and Light Chain Chimeric Antibodies from Example 1 1.
  • Figure 56A shows neutralization activity of Heavy and Light Chain Chimeric
  • Antibodies chimeric pairings 1-32 (from Figure 55).
  • Figure 56B shows Neutralization Activity on New Pairings in rows 33-67 (from Figure 55).
  • Figure 56C shows Neutralization Activity on New Pairings in rows 68-91 (from Figure 55).
  • Figure 56D shows that 8 chimeric antibodies were selected for large scale expression and neutralization activity analysis.
  • Figure 57 shows nucleic acid and amino acid sequences of VH and VL sequences of antibodies from Example 10 (SEQ ID NOs: 263-300).
  • Figure 58 shows sequences of DH51 l_5a and 5b as Fabs (SEQ ID NOs: 301-304).
  • Figures 59A-F show isolation of MPER-directed broadly neutralizing antibodies,
  • Figures 60A-E shows structural analysis of the DH511 lineage, (a) Ribbon model of crystal structures of DH511.1 and DH511.2 Fabs in complex with gp41 MPER peptides 656- 683 and 662-683, respectively, oriented based on Ca-atom superposition of distal MPER residues 671-683. (b) Close-up view of antibody -peptide contacts.
  • gp41 residues that interact with antibody VH3-15 region residues, HCDR3 residues, or both, are shown in cyan, red, and brown, respectively.
  • (c) Ribbon model of crystal structures of Fabs of plasma-derived variants DH511.1 IP and DH511.12P are shown in complex with gp41 MPER peptide 662- 683 [511.1 IP is placeholder here]. Residues shown in surface representation differ in sequence from DH511.1 or DH511.2.
  • Residues that contact gp41 are labeled with closed circles, and somatically-mutated residues shaded red, orange blue, and green, for 10E8, DH511.1, DH511.2, and DH511.1 IP and DH511.12P, respectively.
  • Figures 61A-E shows comparison with other MPER-specific antibodies, (a) Crystal structures of DH511.1 and DH511.2 Fab in complex with gp41 MPER peptides 656-683 and 662-683, respectively, oriented based on Ca-atom superposition of distal MPER residues 671-683. (b) Crystal structures of antibodies 10E8 and 4E10 in complex with MPER peptide epitopes, oriented as in (a), (c) Surface representations of antibodies DH511.1, DH511.2, and 10E8, colored as in (a) and (b) and rotated by 60°. gp41 contact footprints within the HCDR3 loops are colored red and those within the variable heavy chain VH3-15 regions are colored green.
  • VH3-15 contacting residues positions that are shared by antibodies DH511.1 and DH511.2 and antibody 10E8 are colored cyan
  • Figures 62A-C show standard experimental mapping and neutralization-based epitope prediction analysis to delineate the specificities that mediate plasma neutralization breadth
  • Plasma from donor CH0210 showed potent MPER-directed neutralizing activity against the HIV-2/HIV-1 MPER chimeric pseudovirus C1C. Neutralization titer is reported as median inhibitory dilution (ID50).
  • ID50 median inhibitory dilution
  • Anti-MPER antibodies were depleted from plasma using MPER peptide-coated magnetic beads. The depleted fraction was tested for neutralization activity against the indicated heterologous viruses. Neutralization was considerably diminished by removal of anti-MPER from both plasmas, indicating that MPER antibodies were largely responsible for
  • Plasma neutralization breadth is shown, and numbers in each row add up to 1.00. Shown below are the locations on the Env trimer of the epitopes identified by NEP for this donor and confirmed to be targeted by standard experimental mapping methods.
  • Figures 63 A-B show frequency and identity of CDR3 peptides from MPER affinity chromatography
  • Clonotypes were defined as genes with the same V- and J- gene usage and >85% sequence identity in the HCDR3. Frequencies of the identified clonotypes were based on the average peak areas of the detected CDR peptides,
  • (b) Identified clonotypes and gene usage SEQ ID NOs: 311-320).
  • Figure 64 shows Phylogenetic tree of VHDHJH sequences of memory B cell and plasma-derived DH511 clonal lineage members.
  • Figure 65A and 65B show Epitope mapping by alanine scanning mutagenesis of C- terminal MPER residues. Values listed are mean measurements from two independent experiments. Epitope residues were defined as residues where log AUC relative to wild-type (WT) for alanine mutations was reduced by 50%.
  • Figure 66A-C show Surface-plasmon resonance analysis of binding of the DH511 clonal lineage to MPR.03 peptide.
  • Figure 66C shows Association (ka) and dissociation (kd) rate constants and binding affinities (Kd) for each Fab.
  • Figure 67A-C show Surface-plasmon resonance analysis of binding of the DH511 clonal lineage to MPER liposomes (SEQ ID NOs: 321-325).
  • Figure 68A-C show poly/autoreactivity analysis of MPER bNAbs. Reactivity of DH511 clonal lineage members with self-antigens as measured by indirect
  • DH511.1 UC A reacted with ribonucleoprotein
  • DH511 16 reacted with dsDNA.
  • PPP1R1C protein phosphatase 1, regulatory (inhibitor) subunit 1C
  • FYN FYN oncogene related to SRC, FGR, YES, transcription variant 1 [DH511.1,
  • Figure 69 shows ELISA binding of DH511 lineage members to Ul snRNP components.
  • the DH51 l UCA bound specifically to Ul-snRNPA while no binding was observed to the other components. Results shown represent one experiment.
  • Figure 70 shows potential mechanistic differences in binding of 4E10 versus
  • FIG. 71A-C show DH511.2 recognizes a transiently exposed intermediate state of gp41, and the lifetime of DH511.2 epitope exposure is the same as that of 10E8 and 4E10.
  • Time course of neutralization of tier 2 HIV-1 isolate B.BG1168 was measured by addition of mAbs to TZM-bl cells pre-incubated with virus. Half-life values were similar among the three antibodies.
  • Figure 72 shows Sequence Comparison of DH511, DH512, and 10E8 HCDR3 Loops (SEQ ID NOs: 326-328). The figure shows that while HCDR3 loops of DH511 and 10E8 lineages are both encoded by D3-3 precursor, substantial differences are observed in their final matured lengths and sequences.
  • One conserved sequence motif between DH511/DH512 and 10E8 HCDR3s appears to be a hydrophobic residue doublet at the center of the loop (boxed).
  • Figure 73A-D shows Structural Comparison of DH511 (A), DH512 (B), and 10E8 (QHCDR3 Loops. conserveed DH511/DH512 and 10E8 hydrophobic residue doublets at apex of HCDR3 loops are spatially co-localized (D), relative to MPER. Comparison is based on Ca superposition of MPER residues 671-683.
  • Figures 74A-B shows Comparison of DH511, DH512, and 10E8 HCDR3 Loops, (a) Sequence alignment of HCDR3 loops of DH511, DH512, and 10E8 (SEQ ID NOs: 329-331). (b) Structural comparison of HCDR3 loops based on alignment of distal MPER gp41 residues (that CDRH3 orientation differs from Figure 73).
  • the HCDR3 loops of bNabs that target the gp41 MPER have been shown to be critical for their capacity to neutralize the HIV-1 virus, largely through interactions with the viral membrane.
  • Figure 75 shows sequence characteristics of MPER antibodies isolated from memory B cells (SEQ ID NOs: 332-359). Figure 75 corresponds to Supplementary Table 1 as referenced in Example 12.
  • Figure 76 shows neutralization activity of MPER mAbs against a cross-clade 30 isolate HIV-1 Env-pseudovirus panel (IC50 values). Figure 76 corresponds to
  • Figure 77 shows neutralization activity of MPER mAbs against a cross-clade 30 isolate HIV-1 Env-pseudovirus panel (IC80 values). Figure 77 corresponds to
  • Figure 78 shows neutralization activity of DH511.2 against a cross-clade 199 isolate HIV-1 Env-pseudovirus panel.
  • Figure 78 corresponds to Supplementary Table 3 as referenced in Example 12.
  • Figure 79 shows neutralization activity of DH511.2 against a panel of 200 clade C HIV-1 primary isolates.
  • Figure 79 corresponds to Supplementary Table 4 as referenced in Example 12.
  • Figure 80 shows neutralization activity of 16 DH511.2 heavy chain mutant antibodies.
  • Figure 80 corresponds to Supplementary Table 27 as referenced in Example 12.
  • Figure 81 shows sequence characteristics and pairing of plasma-derived heavy and light chains identified by mass spectrometry and paired VH-VL next-generation sequencing (SEQ ID NOs: 360-367).
  • Figure 81 corresponds to Supplementary Table 6 as referenced in Example 12.
  • Figure 82 shows neutralization activity of 16 plasma mAbs against a 4 indicator HIV- 1 Env pseudovirus panel.
  • Figure 82 corresponds to Supplementary Table 7 as referenced in Example 12.
  • Figure 83 shows neutralization activity of plasma mAbs DH511.1 IP and DH511.12P against a cross-clade 203 isolate HIV-1 Env-pseudovirus panel.
  • Figure 83 corresponds to Supplementary Table 8 as referenced in Example 12.
  • Figure 84 shows sequences of alanine substituted MPR.03 peptides (SEQ ID NOs: 368-381). Figure 84 corresponds to Supplementary Table 9 as referenced in Example 12.
  • Figure 85 shows sequences of COT6.15 MPER mutant viruses (SEQ ID NOs: 382- 403). Figure 85 corresponds to Supplementary Table 10 as referenced in Example 12.
  • Figure 86 shows neutralization Activity against a series of MPER alanine mutant pseudoviruses in the COT6.15 Env background.
  • Figure 86 corresponds to Supplementary Table 11 as referenced in Example 12.
  • Figure 87 shows crystallization peptides (SEQ ID NOs: 404-406).
  • Figure 87 corresponds to Supplementary Table 12 as referenced in Example 12.
  • Figure 88 shows cry stall ographic data collection and refinement statistics.
  • Figure 88 corresponds to Supplementary Table 13 as referenced in Example 12.
  • Figure 89 shows antibody contact interfaces by CDR loop.
  • Figure 89 corresponds to
  • Figure 90 shows bonded and non-bonded contacts DH511.1 -MPER. (Non-Kabat numbering). Figure 90 corresponds to Supplementary Table 15 as referenced in Example 12.
  • Figure 91 shows bonded and non-bonded contacts DH511.2-MPER. (Non-Kabat numbering). Figure 91 corresponds to Supplementary Table 16 as referenced in Example 12.
  • Figure 92 shows bonded and non-bonded contacts DH511.11P-MPER.
  • Figure 92 corresponds to Supplementary Table 17 as referenced in Example 12.
  • Figure 93 shows bonded and non-bonded contacts DH511.12P-MPER. (Non-Kabat numbering). Figure 93 corresponds to Supplementary Table 18 as referenced in Example 12.
  • Figure 94 shows neutralization of the DH511 clonal lineage against a panel of 12 global HIV-1 reference strains.
  • Figure 94 corresponds to Supplementary Table 19 as referenced in Example 12.
  • Figures 95A-C show primers and PCR conditions for paired VH:VL NGS.
  • Figure 95A shows overlap extension oligonucleotides for framework region 1 (5' - 3') (SEQ ID NOs: 407-427).
  • Figure 95B shows overlap extension oligonucleotides for leader peptide (5' - 3') (SEQ ID NOs: 428-441).
  • Figure 95C shows nested constant region oligonucleotides (5' - 3') (SEQ ID NOs: 442-446).
  • Figure 95A corresponds to Supplementary Table 28 as referenced in Example 12.
  • Figure 95B corresponds to Supplementary Table 29 as referenced in Example 12.
  • Figure 95C corresponds to Supplementary Table 30 as referenced in Example 12.
  • Figure 96 shows DH511 clonal lineage membrane insertion scores and HCDR3 analysis (SEQ ID NOs: 447-455). The membrane insertion scores can be recalculated to exclude the C in the CDR3. HCDR3s score for the .P antibodies will be calculated.
  • Figure 96 corresponds to Supplementary Table 21 as referenced in Example 12.
  • Figure 97 shows cardiolipin reactivity of the DH511 clonal lineage.
  • Figure 97 corresponds to Supplementary Table 22 as referenced in Example 12.
  • Figure 98 shows neutralization activity of 91 chimeric MPER mAbs against the tier 2 HIV-1 isolate B.BG1168.
  • Figure 98 corresponds to Supplementary Table 23 as referenced in Example 12.
  • Figure 99 shows neutralization activity of chimeric mAb DH511.2 K3 against a cross-clade 30 isolate Env-pseudovirus panel.
  • Figure 99 corresponds to Supplementary Table 24 as referenced in Example 12.
  • Figures lOOA-C show primers and PCR conditions for paired VH:VL NGS.
  • Figure 100A shows PCR conditions for isotype specific amplification.
  • Figure 100B shows oligonucleotides for isotype specific amplification (5' - 3') (SEQ ID NOs: 456-462).
  • Figure lOOC shows PCR conditions for MiSeq Barcoding.
  • Figure 100A corresponds to
  • HIV envelope antibodies Broadly neutralizing and potent HIV envelope antibodies are now being developed for both prevention of HIV (Rudicell RS et al. J. Virol 88: 12669,-82, 2014) and for treatment of HIV infected individuals (Barouch DH, et al. Nature 503 : 224-8, 2013; Shingai M et al. Nature 503 : 277-80, 2013).
  • human recombinant antibodies either alone or in combinations have great prophylactic and therapeutic potential for the prevention and treatment of HIV.
  • antibodies that bind with high affinity to Env may be useful in eliminating the latent pool of HIV -infected CD4 T cells and curing HIV, when either used to sensitize HIV expressing target cells with bispecific bnAbs for NK or CD8 T cell killing or when bnAbs are conjugated with toxins or radionucleotides.
  • the invention provides fully human antibodies and fragments that specifically bind to and potently neutralize various isolates of HIV-1.
  • the antibodies bind to HIV-1 gp41.
  • the antibodies of the invention specifically bind the membrane-proximal extracellular region (MPER) of gp41.
  • MPER membrane-proximal extracellular region
  • the invention provides pharmaceutical compositions including these human antibodies and a pharmaceutically acceptable carrier.
  • the invention provides antibodies for passive immunization against HIV/ AIDS.
  • Nucleic acids encoding these antibodies, expression cassettes and vectors including these nucleic acids, and isolated cells that express the nucleic acids which encode the antibodies of the invention are also provided.
  • the invention provides antibodies which are clonal variants (See e.g., Examples 11, and 12).
  • clonal variants are sequences that differ by one or more nucleotides or amino acids, and have a V region with shared mutations compared to the germline, identical VDJ or VJ gene usage, identical the same or similar HCDR3 length, and the same VL and JL usage.
  • the germline sequence (unmutated common ancestor "UCA") is intended to be the sequence coding for the
  • Intermediate are typically not isolated from a biological sample, but are derived computationally based on VH and/or VL sequences isolated from subjects infected with HIV-1.
  • compositions including the human antibodies of the invention can be used for any purpose including but not limited to research, diagnostic and therapeutic purposes.
  • the human monoclonal antibodies disclosed herein can be used to detect HIV-1 in a biological sample or interfere with the HIV-1 activity, for example to diagnose or treat a subject having an HIV-1 infection and/or AIDS.
  • the antibodies can be used to determine HIV-1 titer in a subject.
  • the antibodies disclosed herein also can be used to study the biology of the human immunodeficiency virus.
  • the antibodies of the invention can be used for therapeutic purposes for treatment or prevention of HIV-1 infection, alone or in combination with other therapeutic modalities, including ART and/or combination with other HIV-1 targeting antibodies, neutralizing antibodies and/or ADCC inducing antibodies.
  • the disclosed MPER antibodies specifically bind to a polypeptide disclosed in for example but not limited to Figure 3, Figure 11, and Figure 16, and Example 12.
  • the person of ordinary skill in the art will understand that the antibodies of the invention can also bind to gp41MPER residues extending N-terminal or C-terminal to the above sequences.
  • residues believed to make contacts with the antibodies of the invention include resides identified in the mapping studies described in for example but not limited to Figures 11, 16-15.
  • the antibodies of the invention are expected to make contact with additional gp41 MPER residues.
  • the antibodies of the invention are expected to make contact with some of the gp41 MPER residues as previously described for the 10E8 antibody.
  • the disclosed antibodies are referred to as 10E8-like antibodies because their binding to the MPER maps to a region similar to the MPER region bound by the 10E8 antibody previously described (See US Pub 20140348785).
  • the 10E8 antibody specifically binds the membrane proximal extracellular region (MPER) of gp41 at an epitope that is designated as the 10E8 epitope.
  • the crystal structure of the 10E8 antibody was solved in complex with a gp41 peptide ( See 20140348785 Example 1), which allowed for detailed analysis of the binding of the 10E8 antibody and gp41, and describe at the atomic level the binding of 10E8 antibody to the 10E8 epitope.
  • This epitope and thus the antibodies of this class (10E8-like antibodies), can be distinguished from other antibodies that bound gp41 at other epitopes.
  • the 10E8 epitope e.g., KWASLWNWFDITNWLWYIR (SEQ ID NO: 464), extends C-terminal to the 2F5 epitope (although there is some overlap) on the gp41 ectodomain and is distinguished from the 4E10 and Z13E1 epitope by expanding the binding to C-terminal residues previously thought to be inaccessible (e.g. these residues were believed to be buried in the lipid bilayer).
  • an MPER antibody of the invention is not the 10E8, 4E10, 2F5 or any other MPER antibody as previously described.
  • Some of the difference between certain antibodies of the invention and the 10E8, 4E10 and 2F5 antibodies are demonstrated in Figure 15 (VH sequence alignment) and Figures 6, and 7 (neutralization breadth and potency), and for example but not limited to Figures 11, 16-25 (epitope mapping studies), Example 12.
  • the inventive antibodies bind an MPER epitope which comprises D674 (See Figure 11).
  • the 10E8 antibody See US Pub 20140348785) MPER binding is not sensitive to D674S mutation.
  • the DH511 lineage antibodies ( Figure 6) neutralize 100% of isolates whereas 10E8 did not ( Figure 7).
  • the antibodies of the invention are expected not to exhibit self- reactivity— they do not bind or bind very weakly to self-antigens, such as human protein.
  • self-antigens such as human protein.
  • Figs. 35-36, Example 12 what matters is whether the mature antibody will be polyreactive or not.
  • Various assays to determine poly and autoreactivity are known in the art.
  • the neutralization breadth of the inventive antibodies is demonstrated by the diversity of viruses which are neutralized in the TZMbl Env pseudovirus inhibition assay.
  • the neutralization breadth and/or binding of the antibodies of the invention can be maintained in the presence of tolerate changes to the epitope. Comparing the sequences of the neutralized viruses, versus viruses that are not neutralized, a skilled artisan can readily determine the % virus changes, including changes in the MPER region and the epitope, which can be tolerated while neutralization and/or binding is maintained.
  • sequence identity is frequently measured in terms of percentage identity (or similarity or homology); the higher the percentage, the more similar the two sequences are.
  • homology is frequently measured in terms of percentage identity (or similarity or homology); the higher the percentage, the more similar the two sequences are.
  • homology is frequently measured in terms of percentage identity (or similarity or homology); the higher the percentage, the more similar the two sequences are.
  • homologs or variants of a polypeptide will possess a relatively high degree of sequence identity when aligned using standard methods.
  • NCBI Basic Local Alignment Search Tool (BLAST) (Altschul et al., J. Mol. Biol. 215:403, 1990) is available from several sources, including the National Center for
  • Homologs and variants of a VL or a VH of an antibody that specifically binds a polypeptide are typically characterized by possession of at least about 75%, for example at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity counted over the full length alignment with the amino acid sequence of interest.
  • Proteins with even greater similarity to the reference sequences will show increasing percentage identities when assessed by this method, such as at least 80%, at least 85%, at least 90%), at least 95%, at least 98%, or at least 99% sequence identity.
  • homologs and variants When less than the entire sequence is being compared for sequence identity, homologs and variants will typically possess at least 80% sequence identity over short windows of 10-20 amino acids, and may possess sequence identities of at least 85% or at least 90% or 95% depending on their similarity to the reference sequence. Methods for determining sequence identity over such short windows are available at the NCBI website on the internet. One of skill in the art will appreciate that these sequence identity ranges are provided for guidance only; it is entirely possible that strongly significant homologs could be obtained that fall outside of the ranges provided.
  • the invention provides antibodies which are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80%) identical to the VH and VL amino acid sequences of the antibodies described herein and still maintain the neutralization breadth, biding and/or potency.
  • the invention provides antibodies which are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80% identical to the CDR1, 2, and/or 3 of VH and CDR1, 2, and/or 3 VL amino acid sequences of the antibodies described herein and still maintain the neutralization breadth, biding and/or potency.
  • the invention provides antibodies which can tolerate a larger percent variation in the sequences outside of the VH and/VL sequences of the antibodies.
  • the invention provides antibodies which are 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80%, 79%, 78%, 77%, 76%, 75%, 74%, 73%, 72%, 71%, 70%, 69%, 68%, 67%, 66%, 65% identical, wherein the identity is outside of the VH or VL regions, or the CDRs of the VH or VL chains of the antibodies described herein.
  • Antibodies exist, for example as intact immunoglobulins and antigen binding variants or fragments e,g. as a number of well characterized produced by digestion with various peptidases. For instance, Fabs, Fvs, scFvs that specifically bind to gp41 or fragments of gp41 would be gp41 -specific binding agents. Binding specificity can be determined by any suitable assay in the art, for example but not limited competition binding assays, epitope mapping, etc.
  • a scFv protein is a fusion protein in which a light chain variable region of an immunoglobulin and a heavy chain variable region of an immunoglobulin are bound by a linker, while in dsFvs, the chains have been mutated to introduce a disulfide bond to stabilize the association of the chains.
  • Provided are also genetically engineered forms such as chimeric antibodies and heteroconjugate antibodies such as bispecific antibodies. See also, Pierce Catalog and Handbook, 1994-1995 (Pierce Chemical Co., Rockford, 111.); Kuby, Immunology, 3.sup.rd Ed., W.H. Freeman & Co., New York, 1997.
  • the invention provides antibody fragments, which have the binding specificity and/or properties of the inventive antibodies.
  • Non-limiting examples include: (1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain; (2) Fab', the fragment of an antibody molecule obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab' fragments are obtained per antibody molecule; (3) (Fab 1 ), sub.2, the fragment of the antibody obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; (4) F(ab').sub.2, a dimer of two Fab' fragments held together by two disulfide bonds; (5) Fv, a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and (6) single chain antibody (“SCA”), a genetically engineered molecule
  • VH refers to the variable region of an immunoglobulin heavy chain, including but not limited to that of an antibody fragment, such as Fv, scFv, dsFv or Fab.
  • VL refers to the variable region of an immunoglobulin light chain, including but not limited to that of an Fv, scFv, dsFv or Fab.
  • nucleic acids encoding any of the antibodies, or fragment thereof can be expressed in a recombinantly engineered cell such as bacteria, plant, yeast, insect and mammalian cells.
  • the nucleic acid sequences include any sequence necessary for expression, including but not limited to a promoter, a leader sequence.
  • These antibodies can be expressed as individual VH and/or VL chain, or can be expressed as a fusion protein.
  • the antibodies can be expressed by viral vector mediated delivery of genes encoding the antibodies of the invention (See e.g. Yang et al. Viruses 2014, 6, 428- 447).
  • scFv single chain antibody
  • the VH- and VL-encoding DNA fragments are operatively linked to another fragment encoding a flexible linker, e.g., encoding the amino acid sequence (Gl Y 4 -Ser) 3 , such that the VH and VL sequences can be expressed as a contiguous single-chain protein, with the VH and VL domains joined by the flexible linker (see, e.g., Bird et al., Science 242:423-426, 1988; Huston et al., Proc. Natl. Acad. Sci. USA 85:5879-5883, 1988; McCafferty et al., Nature 348:552-554, 1990).
  • a cleavage site can be included in a linker, such as a furin cleavage site.
  • a single chain antibody may be monovalent, if only a single VH and VL are used, bivalent, if two VH and VL are used, or polyvalent, if more than two VH and VL are used.
  • Bispecific or polyvalent antibodies may be generated that bind specifically to gpl20 and to another molecule, such as gp41.
  • the invention provides monoclonal antibodies.
  • the monoclonal antibodies are produced by a clone of B -lymphocytes.
  • the monoclonal antibody is a recombinant and is produced by a host cell into which the light and heavy chain genes of a single antibody have been transfected. Any suitable cell could be used for transfection and expression of the antibodies of the invention. Suitable cell lines include without limitation 293T cells or CHO cells.
  • Monoclonal antibodies are produced by any suitable method known to those of skill in the art.
  • monoclonal antibodies are produced by immortalizing B- cell expressing an antibody. Methods for immortalizing B-cells are known in the art, for example but not limited to using EBV transformation, treatment with various stimulants, and/or apoptotic inhibitors (Bonsignori et al. J. Virol. 85: 9998-10009, 2011).
  • monoclonal antibodies are produced by making hybrid antibody-forming cells from a fusion of myeloma cells with immune spleen cells to make hybridomas.
  • monoclonal antibodies are isolated from a subject, for example but not limited as described in Example 1 (Liao HX et al. J Virol Methods. 2009 Jun; 158(l-2): 171-9).
  • the amino acid and nucleic acid sequences of such monoclonal antibodies can be determined.
  • the antibodies described herein, or fragments thereof, may be recombinantly produced in prokaryotic or eukaryotic expression systems. These systems are well described in the art.
  • protein therapeutics are produced from mammalian cells. The most widely used host mammalian cells are Chinese hamster ovary (CHO) cells and mouse myeloma cells, including NSO and Sp2/0 cells.
  • the invention provides an antibody, or antibody fragment, that is recombinantly produced from a mammalian cell-line, including a CHO cell-line.
  • the invention provides a composition comprising an antibody, or antibody fragment, wherein the antibody or antibody fragment was recombinantly produced in a mammalian cell-line, and wherein the antibody or antibody fragment is present in the composition at a concentration of at least 1, 10, 100, 1000 micrograms/mL, or at a
  • concentration of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 milligrams/mL.
  • the antibody composition comprises less than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 50, or 100 nanograms of host cell protein (i.e., proteins from the cell-line used to recombinantly produce the antibody)).
  • the antibody composition comprises less than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 ng of protein A per milligram of antibody or antibody fragment (i.e., protein A is a standard approach for purifying antibodies from recombinant cell culture, but steps should be done to limit the amount of protein A in the composition, as it may be immunogenic).
  • protein A is a standard approach for purifying antibodies from recombinant cell culture, but steps should be done to limit the amount of protein A in the composition, as it may be immunogenic.
  • U.S. Patent No. 7,458,704 Reduced protein A leaching during protein A affinity chromatography; which is hereby incorporated-by-reference.
  • the antibodies of the invention can be of any isotype.
  • the antibodies of the invention can be used as IgGl, IgG2, IgG3, IgG4, whole IgGl or IgG3s, whole monomeric IgAs, dimeric IgAs, secretory IgAs, IgMs as monomeric, pentameric or other polymer forms of IgM.
  • the class of an antibody comprising the VH and VL chains described herein can be specifically switched to a different class of antibody by methods known in the art.
  • the nucleic acid encoding the VH and VL can encode an Fc domain (immunoadhesin).
  • the Fc domain can be an IgA, IgM or IgG Fc domain.
  • the Fc domain can be an optimized Fc domain, as described in U.S. Published Patent Application No. 20100093979, incorporated herein by reference.
  • the immunoadhesin is an IgGl Fc.
  • the immunoadhesin is an IgG3 Fc.
  • the antibodies comprise amino acid alterations, or combinations thereof, for example in the Fc region outside of epitope binding, which alterations can improve their properties.
  • Fc modifications are known in the art. Amino acid numbering is according to the EU Index in Kabat.
  • the invention contemplates antibodies comprising mutations that affect neonatal Fc receptor (FcRn) binding, antibody half-life, and localization and persistence of antibodies at mucosal sites. See e.g. Ko SY et al., Nature 514: 642-45, 2014, at Figure la and citations therein; Kuo, T. and Averson, V., mAbs 3(5): 422-430, 2011, at Table 1, US Pub 20110081347 (an aspartic acid at Kabat residue 288 and/or a lysine at Kabat residue 435), US Pub
  • the antibodies comprise AAAA substitution in and around the Fc region of the antibody that has been reported to enhance ADCC via NK cells (AAA mutations) containing the Fc region aa of S298A as well as E333A and K334A (Shields RI et al JBC , 276: 6591-6604, 2001) and the 4 th A (N434A) is to enhance FcR neonatal mediated transport of the IgG to mucosal sites (Shields RI et al. ibid).
  • Other antibody mutations have been reported to improve antibody half-life or function or both and can be incorporated in sequences of the antibodies.
  • modifications such as but not limited to antibody fucosylation, may affect interaction with Fc receptors (See e.g. Moldt, et al. JVI 86(11): 66189-6196, 2012).
  • the antibodies can comprise modifications, for example but not limited to glycosylation, which reduce or eliminate polyreactivity of an antibody. See e.g. Chuang, et al. Protein Science 24: 1019-1030, 2015.
  • the antibodies can comprise modifications in the Fc domain such that the Fc domain exhibits, as compared to an unmodified Fc domain enhanced antibody dependent cell mediated cytotoxicity (ADCC); increased binding to Fc.gamma.RIIA or to Fc.gamma.RIIIA; decreased binding to
  • ADCC unmodified Fc domain enhanced antibody dependent cell mediated cytotoxicity
  • Fc.gamma.RIIB or increased binding to Fc.gamma.RIIB. See e.g. US Pub 20140328836.
  • antibodies of the invention including but not limited to antibodies comprising a CDR(s) of VH and/or VL chains, or antibody fragments of the inventive antibodies can be used as the HIV-1 binding arm(s) of a bispecific molecule, e.g. DARTS, diabodies, toxin labeled HIV-1 binding molecules.
  • a bispecific molecule e.g. DARTS, diabodies, toxin labeled HIV-1 binding molecules.
  • either the intact antibody or a fragment thereof can be used.
  • Either single chain Fv, bispecific antibody for T cell engagement, or chimeric antigen receptors can be used (Chow et al, Adv. Exp. Biol. Med. 746: 121-41 (2012)). That is, in non-limiting embodiments, intact antibody, a Fab fragment, a diabody, or a bispecific whole antibody can be used to inhibit HIV-1 infection in a subject (e.g., a human).
  • a bispecific F(ab) 2 can also be used with one arm a targeting molecule like CD3 to deliver it to T cells and the other arm the arm of the native antibody (Chow et al, Adv. Exp. Biol.
  • Toxins that can be bound to the antibodies or antibody fragments described herein include unbound antibody, radioisotopes, biological toxins, boronated dendrimers, and immunoliposomes (Chow et al, Adv. Exp. Biol. Med. 746: 121-41 (2012)).
  • Toxins e.g., radionucleotides or other radioactive species
  • can be conjugated to the antibody or antibody fragment using methods well known in the art can be used.
  • the invention also includes variants of the antibodies (and fragments) disclosed herein, including variants that retain the ability to bind to recombinant Env protein, the ability to bind to the surface of virus-infected cells and/or ADCC-mediating properties of the antibodies specifically disclosed, and methods of using same to, for example, reduce HIV-1 infection risk.
  • Combinations of the antibodies, or fragments thereof, disclosed herein can also be used in the methods of the invention.
  • Antibodies of the invention and fragments thereof can be produced recombinantly using nucleic acids comprising nucleotide sequences encoding VH and VL sequences selected from those shown in the figures and examples.
  • the invention provides intact/whole antibodies.
  • the invention provides antigen binding fragments thereof. Typically, fragments compete with the intact antibody from which they were derived for specific binding to the target including separate heavy chains, light chains Fab, Fab', F(ab').sub.2, F(ab)c, diabodies, Dabs, nanobodies, and Fv. Fragments can be produced by recombinant DNA techniques, or by enzymatic or chemical separation of intact immunoglobulins.
  • the invention provides a bispecific antibody.
  • a bispecific or bifunctional/dual targeting antibody is an artificial hybrid antibody having two different heavy /light chain pairs and two different binding sites (see, e.g., Romain Rouet & Daniel Christ “Bispecific antibodies with native chain structure” Nature Biotechnology 32, 136-137 (2014); Garber “Bispecific antibodies rise again” Nature Reviews Drug Discovery 13, 799- 801 (2014), Figure la; Byrne et al. "A tale of two specificities: bispecific antibodies for therapeutic and diagnostic applications” Trends in Biotechnology, Volume 31, Issue 11, November 2013, Pages 621-632 Songsivilai and Lachmann, Clin. Exp.
  • the bispecific antibody is a whole antibody of any isotype. In other embodiments it is a bispecific fragment, for example but not limited to F(ab) 2 fragment. In some embodiments, the bispecific antibodies do not include Fc portion, which makes these diabodies relatively small in size and easy to penetrate tissues.
  • the bispecific antibodies could include Fc region.
  • Fc bearing diabodies for example but not limited to Fc bearing DARTs are heavier, and could bind neonatal Fc receptor, increasing their circulating half-life. See Garber "Bispecific antibodies rise again” Nature Reviews Drug Discovery 13, 799-801 (2014), Figure la; See US Pub 20130295121, incorporated by reference in their entirety.
  • the invention encompasses diabody molecules comprising an Fc domain or portion thereof (e.g. a CH2 domain, or CH3 domain).
  • the Fc domain or portion thereof may be derived from any immunoglobulin isotype or allotype including, but not limited to, IgA, IgD, IgG, IgE and IgM.
  • the Fc domain (or portion thereof) is derived from IgG.
  • the IgG isotype is IgGl, IgG2, IgG3 or IgG4 or an allotype thereof.
  • the diabody molecule comprises an Fc domain, which Fc domain comprises a CH2 domain and CH3 domain independently selected from any immunoglobulin isotype (i.e. an Fc domain comprising the CH2 domain derived from IgG and the CH3 domain derived from IgE, or the CH2 domain derived from IgGl and the CH3 domain derived from IgG2, etc.).
  • the Fc domain may be engineered into a polypeptide chain comprising the diabody molecule of the invention in any position relative to other domains or portions of the polypeptide chain (e.g., the Fc domain, or portion thereof, may be c-terminal to both the VL and VH domains of the polypeptide of the chain; may be n-terminal to both the VL and VH domains; or may be N-terminal to one domain and c-terminal to another (i.e., between two domains of the polypeptide chain)).
  • the Fc domain, or portion thereof may be c-terminal to both the VL and VH domains of the polypeptide of the chain; may be n-terminal to both the VL and VH domains; or may be N-terminal to one domain and c-terminal to another (i.e., between two domains of the polypeptide chain)).
  • the present invention also encompasses molecules comprising a hinge domain.
  • the hinge domain be derived from any immunoglobulin isotype or allotype including IgA, IgD, IgG, IgE and IgM.
  • the hinge domain is derived from IgG, wherein the IgG isotype is IgGl, IgG2, IgG3 or IgG4, or an allotype thereof.
  • the hinge domain may be engineered into a polypeptide chain comprising the diabody molecule together with an Fc domain such that the diabody molecule comprises a hinge-Fc domain.
  • the hinge and Fc domain are independently selected from any immunoglobulin isotype known in the art or exemplified herein. In other embodiments the hinge and Fc domain are separated by at least one other domain of the polypeptide chain, e.g., the VL domain.
  • the hinge domain, or optionally the hinge-Fc domain may be engineered in to a polypeptide of the invention in any position relative to other domains or portions of the polypeptide chain.
  • a polypeptide chain of the invention comprises a hinge domain, which hinge domain is at the C-terminus of the polypeptide chain, wherein the polypeptide chain does not comprise an Fc domain.
  • a polypeptide chain of the invention comprises a hinge-Fc domain, which hinge-Fc domain is at the C- terminus of the polypeptide chain. In further embodiments, a polypeptide chain of the invention comprises a hinge-Fc domain, which hinge-Fc domain is at the N-terminus of the polypeptide chain.
  • the invention encompasses multimers of polypeptide chains, each of which polypeptide chains comprise a VH and VL domain, comprising CDRs as described herein.
  • the VL and VH domains comprising each polypeptide chain have the same specificity, and the multimer molecule is bivalent and monospecific.
  • the VL and VH domains comprising each polypeptide chain have differing specificity and the multimer is bivalent and bispecific.
  • the polypeptide chains in multimers further comprise an Fc domain.
  • Fc domains Dimerization of the Fc domains leads to formation of a diabody molecule that exhibits immunoglobulin-like functionality, i.e., Fc mediated function (e.g., Fc-Fc.gamma.R interaction, complement binding, etc.).
  • Fc mediated function e.g., Fc-Fc.gamma.R interaction, complement binding, etc.
  • diabody molecules of the invention encompass tetramers of polypeptide chains, each of which polypeptide chain comprises a VH and VL domain.
  • two polypeptide chains of the tetramer further comprise an Fc domain.
  • the tetramer is therefore comprised of two ' heavier polypeptide chains, each comprising a VL, VH and Fc domain, and two lighter polypeptide chains, comprising a VL and VH domain. Interaction of a heavier and lighter chain into a bivalent monomer coupled with dimerization of the monomers via the Fc domains of the heavier chains will lead to formation of a tetravalent immunoglobulin-like molecule.
  • the monomers are the same, and the tetravalent diabody molecule is monospecific or bispecific. In other aspects the monomers are different, and the tetra valent molecule is bispecific or tetraspecific.
  • Formation of a tetraspecific diabody molecule as described supra requires the interaction of four differing polypeptide chains. Such interactions are difficult to achieve with efficiency within a single cell recombinant production system, due to the many variants of potential chain mispairings.
  • One solution to increase the probability of mispairings is to engineer "knobs-into-holes" type mutations into the desired polypeptide chain pairs. Such mutations favor heterodimerization over homodimerization.
  • an amino acid substitution (preferably a substitution with an amino acid comprising a bulky side group forming a ' knob ' , e.g., tryptophan) can be introduced into the CH2 or CH3 domain such that steric interference will prevent interaction with a similarly mutated domain and will obligate the mutated domain to pair with a domain into which a complementary, or accommodating mutation has been engineered, i.e., ' the hole ' (e.g., a substitution with glycine).
  • Such sets of mutations can be engineered into any pair of polypeptides comprising the diabody molecule, and further, engineered into any portion of the polypeptides chains of the pair.
  • Bispecific Antibody Highly Efficient Heterodimerization, Expression And Tumor Cell Lysis," J. Immunol. Methods 296:95-101; each of which is hereby incorporated herein by reference in its entirety).
  • the invention also encompasses diabody molecules comprising variant Fc or variant hinge-Fc domains (or portion thereof), which variant Fc domain comprises at least one amino acid modification (e.g. substitution, insertion deletion) relative to a comparable wild-type Fc domain or hinge-Fc domain (or portion thereof).
  • Molecules comprising variant Fc domains or hinge-Fc domains (or portion thereof) e.g., antibodies
  • the variant phenotype may be expressed as altered serum half-life, altered stability, altered susceptibility to cellular enzymes or altered effector function as assayed in an NK dependent or macrophage dependent assay.
  • Fc domain variants identified as altering effector function are known in the art. For example International Application WO04/063351, U.S. Patent Application Publications 2005/0037000 and 2005/0064514.
  • the bispecific diabodies of the invention can simultaneously bind two separate and distinct epitopes.
  • the epitopes are from the same antigen.
  • the epitopes are from different antigens.
  • at least one epitope binding site is specific for a determinant expressed on an immune effector cell (e.g. CD3, CD16, CD32, CD64, etc.) which are expressed on T lymphocytes, natural killer (NK) cells or other mononuclear cells.
  • an immune effector cell e.g. CD3, CD16, CD32, CD64, etc.
  • NK natural killer
  • diabody molecules of the invention may exhibit Ig-like functionality independent of whether they further comprise an Fc domain (e.g., as assayed in any effector function assay known in the art or exemplified herein (e.g., ADCC assay).
  • Fc domain e.g., as assayed in any effector function assay known in the art or exemplified herein (e.g., ADCC assay).
  • Non-limiting examples of bispecific antibodies can also be (1) a dual-variable-domain antibody (DVD-Ig), where each light chain and heavy chain contains two variable domains in tandem through a short peptide linkage (Wu et al., Generation and Characterization of a Dual Variable Domain Immunoglobulin (DVD-Ig.
  • DVD-Ig dual-variable-domain antibody
  • TM. Molecule, In: Antibody Engineering, Springer Berlin Heidelberg (2010)); (2) a Tandab, which is a fusion of two single chain diabodies resulting in a tetravalent bispecific antibody that has two binding sites for each of the target antigens; (3) a flexibody, which is a combination of scFvs with a diabody resulting in a multivalent molecule; (4) a so called "dock and lock" molecule, based on the
  • “dimerization and docking domain” in Protein Kinase A which, when applied to Fabs, can yield a trivalent bispecific binding protein consisting of two identical Fab fragments linked to a different Fab fragment; (5) a so-called Scorpion molecule, comprising, e.g., two scFvs fused to both termini of a human Fc-region.
  • platforms useful for preparing bispecific antibodies include but are not limited to BiTE (Micromet), DART (MacroGenics) (e,g, US Patent 8,795,667; U.S. Publication Nos. 2014-0099318; 2013-0295121; 2010- 0174053 and 2009-0060910; European Patent Publication No.
  • the bispecific antibody comprises an HIV envelope binding fragment, for example but not limited to an HIV envelope binding fragment from any of the antibodies described herein.
  • the bispecific antibody further comprises a second antigen-interaction-site/fragment.
  • the bispecific antibody further comprises at least one effector domain.
  • the bispecific antibodies engage cells for Antibody- Dependent Cell-mediated Cytotoxicity (ADCC).
  • ADCC Antibody- Dependent Cell-mediated Cytotoxicity
  • the bispecific antibodies engage natural killer cells, neutrophil polymorphonuclear leukocytes, monocytes and macrophages.
  • the bispecific antibodies are T-cell engagers.
  • the bispecific antibody comprises an HIV envelope binding fragment and CD3 binding fragment.
  • CD3 antibodies are known in the art. See for example US Patent 8,784,821.
  • the bispecific antibody comprises an HIV envelope binding fragment and CD 16 binding fragment.
  • the invention provides antibodies with dual targeting specificity.
  • the invention provides bi-specific molecules that are capable of localizing an immune effector cell to an HIV-1 envelope expressing cell, so as facilitate the killing of the HIV-1 envelope expressing cell.
  • bispecific antibodies bind with one "arm” to a surface antigen on target cells, and with the second "arm” to an activating, invariant component of the T cell receptor (TCR) complex. The simultaneous binding of such an antibody to both of its targets will force a temporary interaction between target cell and T cell, causing activation of any cytotoxic T cell and subsequent lysis of the target cell.
  • the immune response is re-directed to the target cells and is independent of peptide antigen presentation by the target cell or the specificity of the T cell as would be relevant for normal MHC-restricted activation of CTLs.
  • immunological synapse is mimicked.
  • Particularly desirable are bispecific antibodies that do not require lymphocyte preconditioning or co-stimulation in order to elicit efficient lysis of target cells.
  • BiTE bispecific T cell engager
  • bispecific formats being evaluated for T cell engagement include diabodies (Holliger et al., Prot Eng 9, 299-305 (1996)) and derivatives thereof, such as tandem diabodies
  • DART dual affinity retargeting
  • the so-called triomabs which are whole hybrid mouse/rat IgG molecules and also currently being evaluated in clinical trials, represent a larger sized format (reviewed in Seimetz et al., Cancer Treat Rev 36, 458-467 (2010)).
  • the invention also contemplates bispecific molecules with enhanced pharmacokinetic properties. In some embodiments, such molecules are expected to have increased serum half- life. In some embodiments, these are Fc-bearing DARTs (see supra).
  • such bispecific molecules comprise one portion which targets HIV-1 envelope and a second portion which binds a second target.
  • the first portion comprises VH and VL sequences, or CDRs from the antibodies described herein.
  • the second target could be, for example but not limited to an effector cell.
  • the second portion is a T-cell engager.
  • the second portion comprises a sequence/paratope which targets CD3.
  • the second portion is an antigen-binding region derived from a CD3 antibody, optionally a known CD3 antibody.
  • the anti-CD antibody induce T cell-mediated killing.
  • the bispecific antibodies are whole antibodies.
  • the dual targeting antibodies consist essentially of Fab fragments. In other embodiments, the dual targeting antibodies comprise a heavy chain constant region (CHI . In certain embodiments, the bispecific antibody does not comprise Fc region. In certain embodiments, the bispecific antibodies have improved effector function. In certain embodiments, the bispecific antibodies have improved cell killing activity.
  • CHI heavy chain constant region
  • Various methods and platforms for design of bispecific antibodies are known in the art. See for example US Pub. 20140206846, US Pub. 20140170149, US Pub. 20090060910, US Pub 20130295121, US Pub. 20140099318, US Pub. 20140088295 which contents are herein incorporated by reference in their entirety.
  • the invention provides human, humanized and/or chimeric antibodies.
  • the invention provides a pharmaceutical composition comprising an antibody of the invention wherein the composition is used for therapeutic purposes such as but not limited to prophylaxis, treatments, prevention, and/or cure.
  • the invention provides a pharmaceutical composition comprising an antibody of the invention in combination with any other suitable antibody.
  • the pharmaceutical compositions comprise nucleic acids which encode the antibodies of the invention. In certain embodiments, these nucleic acids can be expressed by any suitable vector for expression of antibodies.
  • Non-limiting examples include attenuated viral hosts or vectors or bacterial vectors, recombinant vaccinia virus, adenovirus, adeno-associated virus (AAV), herpes virus, retrovirus, cytomegalovirus or other viral vectors can be used to express the antibody.
  • attenuated viral hosts or vectors or bacterial vectors recombinant vaccinia virus, adenovirus, adeno-associated virus (AAV), herpes virus, retrovirus, cytomegalovirus or other viral vectors can be used to express the antibody.
  • compositions include excipient suitable for a biologic molecule such as the antibodies of the invention.
  • excipient suitable for a biologic molecule such as the antibodies of the invention.
  • the antibodies could be produced in specific cell lines and conditions so as to control glycosylation of the antibody.
  • the antibody framework for example, could comprise specific modification so as to increase stability of the antibody.
  • the invention provides that the antibodies, and fragments thereof, described herein can be formulated as a composition (e.g., a pharmaceutical composition).
  • a composition e.g., a pharmaceutical composition.
  • Suitable compositions can comprise an inventive antibody (or antibody fragment) dissolved or dispersed in a pharmaceutically acceptable carrier (e.g., an aqueous medium).
  • the compositions can be sterile and can be in an injectable form (e.g. but not limited to a form suitable for intravenous injection, intramascular injection).
  • the antibodies (and fragments thereof) can also be formulated as a composition appropriate for topical administration to the skin or mucosa.
  • Such compositions can take the form of liquids, ointments, creams, gels and pastes.
  • the antibodies (and fragments thereof) can also be formulated as a composition appropriate for intranasal administration.
  • the antibodies (and fragments thereof) can be formulated so as to be administered as a post-coital douche or with a condom. Standard formulation techniques can be used in preparing suitable compositions.
  • the antibody (and fragments thereof), , described herein have utility, for example, in settings including but not limited to the following: i) in the setting of anticipated known exposure to HIV-1 infection, the antibodies described herein (or fragments thereof) and be administered prophylactically (e.g., IV, topically or intranasally) as a microbiocide, ii) in the setting of known or suspected exposure, such as occurs in the setting of rape victims, or commercial sex workers, or in any homosexual or heterosexual transmission without condom protection, the antibodies described herein (or fragments thereof) can be administered as post-exposure prophylaxis, e.g., IV or topically, and iii) in the setting of Acute HIV infection (AHI), the antibodies described herein (or fragments thereof) can be administered as a treatment for AHI to control the initial viral load or for the elimination of virus-infected CD4 T cells.
  • prophylactically e.g., IV, topically or intranasally
  • the antibodies (or antibody fragments) described herein can be administered prior to contact of the subject or the subject's immune system/cells with HIV-1 or within about 48 hours of such contact. Administration within this time frame can maximize inhibition of infection of vulnerable cells of the subject with HIV- 1.
  • various forms of the antibodies described herein can be administered to chronically or acutely infected HIV patients and used to kill remaining virus infected cells by virtue of these antibodies binding to the surface of virus infected cells and being able to deliver a toxin to these reservoir cells.
  • Suitable dose ranges can depend on the antibody (or fragment) and on the nature of the formulation and route of administration. Optimum doses can be determined by one skilled in the art without undue experimentation. For example, doses of antibodies in the range of 1-50 mg/kg of unlabeled or labeled antibody (with toxins or radioactive moieties ) can be used. If antibody fragments, with or without toxins are used or antibodies are used that can be targeted to specific CD4 infected T cells, then less antibody can be used (e.g., from 5 mg/kg to 0.01 mg/kg).
  • the invention provides use of the antibodies of the invention, including bispecific antibodies, in methods of treating and preventing HIV-1 infection in an individual, comprising administering to said individual a therapeutically effective amount of a composition comprising the antibodies of the invention in a pharmaceutically acceptable form.
  • the methods include a composition which includes more than one HIV-1 targeting antibody.
  • the HIV-1 targeting antibodies in such combination bind different epitopes on the HIV-1 envelope.
  • such combinations of bispecific antibodies targeting more than one HIV-1 epitope provide increased killing of HIV-1 infected cells.
  • such combinations of bispecific antibodies targeting more than one HIV-1 epitope provide increased breadth in recognition of different HIV-1 subtypes.
  • the composition comprising the antibodies of the invention alone or in any combination can be administered via IM, subcutaneous, or IV delivery, or could be deposited at mucosal sites, such as the oral cavity to prevent maternal to child transmission, the rectal space or the vagina as a microbicide.
  • the antibodies can be administered locally in the rectum, vagina, or in the oral cavity, and can be formulated as a microbiocide (Hladik F et al ELIFE Elife. 2015 Feb 3;4. doi: 10.7554/eLife.04525.; Multipurpose prevention technologies for reproductive and sexual health. Stone A. Reprod Health Matters. 2014 Nov;22(44):213-7.
  • antibodies can be formulated such that the therapeutic antibody or combination thereof is impregnated on a vaginal ring (Chen Y et al. Drug Des. Devel. Ther 8: 1801-15, 2014;Malcolm RK et al BJOG 121 Suppl 5: 62-9, 2014). Antibodies can be administered alone or with anti-retroviral drugs for a combination microbiocide (Hladik F et al ELIFE Elife. 2015 Feb 3;4. doi: 10.7554/eLife.04525)
  • the antibodies can be administered in complex with a form of HIV Env, optimally gpl20, but also an Env trimer, to enhance Env immunogenicity.
  • the antibodies can be delivered by viral vector mediated delivery of genes encoding the antibodies of the invention (See e.g. Yang et al. Viruses 2014, 6, 428-447).
  • the antibodies can be administered in viral vector, for example but not limited to adenoassociated viral vector, for expression in muscle and plasma.
  • antibodies with different binding specificities are combined for use in pharmaceutical compositions and therapeutic methods.
  • CD4 binding site antibodies are combined with V3 antibodies, MPER antibodies and so forth.
  • Figures 8, 9 and 10 show a selection of potent HIV-1 neutralizing antibodies which can be used in pharmaceutical compositions, and therapeutic methods.
  • selections of combinations of certain antibodies include: DH542, DH542 L4, DH542 QSA, DH429 and DH512 (or any of the DH512 variants); DH512 and CH31 (See US
  • DH512 or any of the other DH512 variants
  • DH540 See Example 8, and this antibody will be described elsewhere
  • DH542 QSA DH429, DH512 and DH540
  • a polyclonal mixture of Abs is expected reduce or eliminate viral escape.
  • a combination therapy envisions a composition which combines various antibodies.
  • a combination therapy is provided wherein antibodies are administered as individual compositions, for example at different times, by different means, or at administered at different locations.
  • a combination therapy is provides wherein a therapeutic antibody or antibodies is combined with other therapeutic means, for example anti-retroviral drug cocktails, or drugs which activate latently infected HIV-1 cells.
  • the disclosed antibodies or antigen binding fragments thereof are used to determine whether HIV-1 envelope(s) is a suitable antigen for inclusion in a vaccine composition.
  • the antibodies can be used to determine whether an antigen in a vaccine composition including a gp41 immunogen assumes a conformation including an epitope bound by the inventive antibodies or fragments thereof.
  • the detection of the immune complex in the sample indicates that vaccine component, such as a HIV-1 Env antigen assumes a conformation capable of binding the antibody or antigen binding fragment.
  • DH511_5a DH511.12P.
  • Chimeric antibodies which combine a heavy and light chain from different antibodies are typically indicated by the designation of the heavy and light chain of each parent antibody.
  • Figure 1 shows the three HIV infected individual plasma that was evaluated for HIV neutralizing activity and the specificities profiled by the Georgiev algorithm (Georgiev IS et al Science 340: 751-6, 2013). From this analysis we found three subjects (CH0210, CH0536, CH1244) with gp41 bnAb activity (Figure 1).
  • Pairs of VH and VL genes as selected above can also be used to produce plasmids for stable expression of recombinant antibodies.
  • the plasmids or linear constructs for recombinant antibody expression also comprise AAAA substitution in and around the Fc region of the antibody that has been reported to enhance ADCC via K cells (AAA mutations) containing the Fc region aa of S298A as well as E333A and K334A (Shields RI et al JBC , 276: 6591-6604, 2001) and the 4 th A (N434A) is to enhance FcR neonatal mediated transport of the IgG to mucosal sites (Shields RI et al. ibid).
  • the antibodies of the invention were selected based on a combination of criteria including sequence analyses, and functional analyses including but not limited as
  • the antibodies of the invention comprise naturally rearranged VH and VL fragment pairs, wherein the rest of the Ig gene is not naturally occurring with the isolated rearranged VH and VL fragments.
  • the antibodies of the invention are recombinantly produced by synthesized
  • FIG. 4 and Example 12 shows a summary of some of the characteristics of the recombinant MPER antibodies of the invention.
  • DH511-DH517 are antibodies with VH and VL chains from individual CH0210.
  • DH518 is an antibody with VH and VL chains from individual CH0536.
  • DH536 is an antibody with VH and VL chains from individual CH1244.
  • CH537 is an antibody with VH and VL chains from individual CH0585.
  • DH 511-DH516 antibodies are all members of the same B cell clonal lineage (Figure 6).
  • Figure 5 shows the neutralizing capacity of these antibodies with all but DH536 and DH537 able to neutralize difficult to neutralized (tier 2) HIV strains B.BG1168, C.CH505, and C.DU172).
  • Figure 6 shows the phylogram of the DH511 clonal lineage.
  • TZMbl neutralization assay is a standard way to evaluate antibody breadth and potency. See Montefiori, D. Methods Mol Biol. 2009;485:395-405; HIV-1 Env- pseudoviruses infection of TZM-bl cells. Exemplary pseudovirus neutralization assays and panels of HIV-1 pseudovirus are described for example, in Li et al., J Virol 79, 10108- 10125, 2005, Seaman et al, J. Virol., 84: 1439-1452, 2010; Sarzotti-Kelsoe et al., J. Immunol. Methods, 409: 131-46, 2014; and WO2011/038290, each of which is incorporated by reference herein. Various HIV-1 isolates, both Tier 1 and Tier 2 viruses can be included in this assay.
  • the TZMbl assay was conducted to determine neutralization potency and breadth of the various antibodies of the invention on different HIV-1 pseudoviruses.
  • Figure 7 shows the results of neutralization of 8 of the gp41 antibodies against a panel of 30 HIV tier 2 isolates in the TZMbl pseudovirus neutralization assay.
  • the DH511 clonal lineage members all neutralized 100% (30/30) isolates while DH517 neutralized 50% and DH518 neutralized 83%. This in contrast to 10E8 gp41 antibody that only neutralized 29/30 isolates.
  • Figure 8 shows the mean IC50, IC80 and percent of isolates neutralized at an IC50 ⁇ 50ug/ml and at an IC80 of ⁇ 5ug/ml (confirm).
  • mAb DH512 is equally as potent and slightly more broad in neutralization breadth than the mAb 10E8.
  • Figure 9 shows other mAbs and their breadth and potency.
  • Various figures, including without limitation, Figures 37, 38, 28, 56 and 34, and Figures from Example 12 show neutralization data of various antibodies against various panels of pseudoviruses.
  • Example 3 Epitope mapping of MPER antibodies
  • Binding of antibodies to various MPER peptides in an ELISA assay was used to map the epitopes of the MPER antibodies.
  • Figure 11 shows that Antibody epitopes maps to the C-terminus of gp41 to a similar region where 10E8 binds (Huang J et al. Nature 491 406, 2012; See US Pub 20140348785).
  • Figures 11, 15-25 show binding of antibodies to MPER peptide variants.
  • DH512 shows the broadest and most potent neutralization among the antibodies tested.
  • Figure 12 shows an alanine substituted gp41 peptide set used to map DH517 mab and Figure 13 shows a summary of ala mutants to which the antibody is sensitive for binding to gp41.
  • Figures 14 and 15 show the VH and VL sequences of the DH511-DH516 antibodies.
  • Figures 12-13 show the nucleotide and amino acid sequences of all the certain antibodies of the invention.
  • FIGS. 16-25 show that DH517 displayed a unique mapping pattern in that it depends on DKW at the N terminus and several residues at the C terminus important for 10E8 binding and neutralization.
  • Clone DH511 mAbs bound strongly to the majority of the MPER656 variants, showing decreased binding to MPER656.2 and MPER656.2dYIK683R-biotin. These data indicate that the asparagine at position 674 is critical for binding, thus providing evidence that these mAbs bind at the C-terminus.
  • Kd measurements of antibody binding to HIV-1 envelope, e.g. gp41 or any other suitable peptide for the MPER antibodies will be determined by Surface Plasmon Resonance measurements, for example using Biacore, or any other suitable technology which permits detection of interaction between two molecules in a quantitative way.
  • Example 5 Various assays
  • AtheNA Multi-Lyte ANA Plus Test System is one such assay.
  • ELISA cardiolipin assay is another assay to measure autoreactivity.
  • CH557 is one example of a CD4bs broad neutralizing HIV-1 antibody, from a series of clonal antibodies ( Figure 28) which can be used in combination with the antibodies of the invention.
  • Example 7 V3 glycan Antibodies from DH270 lineage
  • Antibodies from DH270 lineage are shown in Figure 26. II (DH270IA1), 12, 14, 13 and UCA in Figure 26 are not isolated from human subjects but are derived computationally based on VH and VL sequences of other observed antibodies from the clone: DH471, DH429, DH473, DH391 and DH270.
  • the VH and VL sequences of DH471, DH429, DH473, DH391 and DH270 are derived from a human subject infected with HIV-1.
  • VH and VL sequences of DH471, DH429, DH473, DH391 and DH270 are derived essentially as described in Example 1, except that cell were sorted with a different hook.
  • DH542, DH542-QSA, DH542 K3 are non-limiting examples of V3 antibodies, which can be used in combination with the antibodies of the invention.
  • the nucleotide and amino acid sequences of the VH and VL of DH542 QSA are shown below.
  • DH542 QSA antibody has the VH of DH542 and the VL called DH542-QSA
  • DH542-L4 is an antibody that has a VH of DH542 and VL of DH429 ( Figure 26)
  • Example 8 DH540 antibody is described elsewhere.
  • DH540 antibody is described in detail in US Ser. No. 62/170,558, filed June 3, 2015.
  • TZMbl neutralization assay was conducted to determine neutralization potency and breadth of different HIV-1 viral species by DH512 and mAb 10E8.
  • Figures 37 and 38 show the results of neutralization against a panel of HIV isolates in the TZMbl pseudovirus neutralization assay.
  • Figures 37 and 38 also show the mean IC50, IC80 and percent of isolates neutralized at different IC50 or IC80 values.
  • Example 10 Isolation of additional antibodies from the DH511 lineage
  • High throughput native VH:VL sequencing from single B cells [0235] Additional antibodies were isolated from the individual CH0210 by high-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. See Figure 39. For detailed methods, see DeKosky et al. Nature Biotechnology, 31, 166-169 (2013), and DeKosky et al. Nature Medicine, 21, 86-91 (2015). Briefly B cells were isolated from PBMCs via negative depletion. The heavy and light chain transcripts were co-localized on RNA binding beads, and then physically tied together using overlap extension RT-PCR. The paired VH:VL amplicons were then used to generate 3 libraries for sequencing: a heavy chain database, a light chain database, and a paired database.
  • F(ab)2 fragments were prepared from total serum IgG and subjected to antigen- affinity chromatography using the MPER peptide. Proteins in the elution and flow-through were denatured and reduced, alkylated, trypsin-digested and analyzed by high resolution LC- MS/MS. Spectra were interpreted with the heavy chain database obtained from next- generation sequencing, and peptides uniquely associated with a single CDR ("informative peptides”) were used to identify full-length VH sequences. Clonotypes are defined as VH sequences having the same germline V and J and at least 85% aa identity in the CDRH3.
  • VH and VL genes were selected and made in linear cassettes (essentially as described in Liao HX et al. J. Virol. Methods 158: 171-9, 2009, see for example Figure 1, Section 3.3) to produce recombinant monoclonal antibodies by transient transfection in 293T cells. See also Example 1 for variations in the backbone.
  • Example 11 Heavy and Light Chain Chimeric Antibodies; Antibodies with changes in the amino acids of the VH chain
  • This example describes chimeric antibodies comprising non-natural VH and VL chain pairs. Naturally occurring VH or VL chain are combined in non-natural pairs as described in Figure 55, chimeras 1-91.
  • DH511 2AVK DH512 K44A
  • VH H5100494A (DH512)
  • VL DH511 5 AVK
  • the invention contemplates antibodies which comprise amino acid changes, or combination of such changes, in the VH chains of antibodies form the DH511 lineage.
  • Non- limiting examples of antibodies with mutations are provided in Figures 30-33, or any combination thereof. Most mutations are to changes to W, but can also try F, L or possibly other substitutions, e.g. without limitation I, V, A. Additional mutations include without limitation the following: TlOOaF; TlOOaL; TlOOal; TlOOaV; TlOOaA; LlOOdW, or any combination thereof.
  • such double mutants TlOOaW-LlOOdF; TlOOaW-LlOOdW; TlOOaF-LlOOdF; TlOOaL-LlOOdF; TlOOaL-LlOOdW.
  • LlOOd could be changed to Trp.
  • Mutated VH chain as contemplated above could be combined with VH chain from DH512, or with VH chain from DH512 K3 (DH511 2AVK).
  • bnAbs broadly reactive neutralizing antibodies
  • MPER envelope gp41 membrane proximal external region
  • mAb 4E10 Monoclonal antibody 4E10, while extremely broad in neutralization breadth, is not potent, and is highly polyreactive with many non-HIV-1 proteins and autoreactive with the human protein splicing factor 3b subunit 3 (SF3B3) (3) as well as with lipids (4).
  • mAb 10E8 is not as polyreactive as 4E10, and is both more broad and potent (1), although it does have a degree of lipid reactivity (5) and is autoreactive with the host protein family of sequence similarity 84 member A (FAM84A) (6).
  • HIV-1 broadly neutralizing antibodies have been isolated from memory B cells, either with clonal memory B cell cultures or using fluorophore-labeled Env and flow cytometry cell sorting.
  • most correlates of protection for infectious agents with successful vaccines are the levels of plasma neutralizing antibodies.
  • the correlate of decreased transmission risk in the only HIV-1 vaccine trial to demonstrate a degree of efficacy was plasma antibodies to the second variable loop (V2) region (7).
  • HIV-1 -specific antibodies In HIV-1 infection, 60% of HIV-1 -specific antibodies derive from abnormal B cell subsets, that are either activated or exhausted and express Fc receptor-like-4 (FcRL4) (8, 9). However, many of the antibodies reflected in HIV-1 memory B cells are not expressed in plasma (8). Similarly, many of the memory B cell specificities of antibodies in other settings are also not represented in plasma (10-12). Thus, it is not known if envelope-reactive memory B cells with bnAb B cell receptors are a major source of plasma broad neutralizing activity.
  • FcRL4 Fc receptor-like-4
  • the DH511 B cell clonal lineage was distinguished by HCDR3 loops of 24 amino acids in DH511.1, DH511.3, and DH511.6, while DH511.2, DH511.4, and DH511.5 antibodies had a one amino acid deletion in the HCDR3, resulting in a length of 23 amino acids (Supplementary Table 1).
  • V H and V L somatic mutation rates were 15-22% and 14-18%>, respectively.
  • the DH511 clonal lineage was derived from the same heavy-chain germ line gene as previously isolated gp41 neutralizing antibody 10E8 (V H 3-15), but utilized a different V L germ line gene (DH511 : V K l-39, 10E8: V L 3-19) (1) (Supplementary Table 1).
  • Antibody DH517 derived from a second clonal lineage arising from the same donor, was similarly isolated.
  • DH517 utilized V H 4-34 and V L 3-19 germ line genes, was 22.8%> and 14.3% mutated, respectively, and had a long HCDR3 comprised of 24 amino acids.
  • DH511.1-DH511.6 and DH517 mAbs were assessed for neutralization breadth and potency against a panel of 30 cross-clade HIV-1 isolates. All six DH511 clonal members neutralized 30 of 30 isolates tested with median 50%> inhibitory concentrations (IC 50 ) ranging from 0.7 to 4.2 ⁇ g/ml (Supplementary Table 2a). DH517 had less breadth than DH511 clone antibodies, neutralizing 15 of 30 isolates with a median IC 50 of 5.7 ⁇ g/ml (Supplementary Table 2a).
  • MPER-specific plasma antibody repertoire from donor CH0210 using an independent proteomics-based approach for the identification and semi-quantitative determination of antigen-specific antibodies in human serum (15, 16).
  • MPER-specific antibodies were isolated from a 2 ml plasma sample by affinity chromatography, processed for proteomics (10) and subjected to liquid chromatography high-resolution tandem mass spectrometry (LC-MS/MS) analysis.
  • V H database comprising 98,413 unique high quality sequences was derived from a natively paired V H :V L repertoire from 845,000 peripheral single B cells from total PBMCs (isolated using MACS negative selection: CD2 " CD14 " CD16 " CD43 " CD235a " ) (17-19). These V H sequences were then clustered into 4,428 clonotypes, using a cut-off of >85% amino acid identity in the HCDR3 region.
  • Clonotype IV comprised 95% of the total intensity of HCDR3 peptides detected in the MPER-specific antibody repertoire (i.e. in antibodies eluted following affinity chromatography with immobilized MPR.03 peptide); we noted that detection of HCDRl and HCDR2 peptides unique to Clonotype IV provided further unambiguous support for the prevalence of these antibodies in the CH0210 plasma (Fig. 59f).
  • Clonotype II which included antibodies DH511.2, DH511.4 and DH511.5 isolated by single- cell sorting, and Clonotype III were detected at 4% and 1% relative abundancy, respectively (Fig. 59f). All three HCDR3 clonotypes utilized the same VDJ genes (V H 3-15, D H 3-3 and 1 ⁇ 26), displayed similar HCDR3 lengths of 23-24 amino acids and V H gene mutation rates of 15-20%) (Supplementary Table 6). Whereas 11 V H DH51 1 clonal lineage members were found by mass spectrometry (Supplementary Table 6, Figure 64), the phylogram was collapsed to represent the most prevalent members (Fig. 59f). It is noteworthy that Clonotype I (Fig.
  • DH511.1, DH511.3 and DH511.6 was isolated by memory B cell sorting but was not detected in the plasma; we validated that recombinant DH511.1, DH511.3 and DH511.6 antibodies were readily detectable by mass spectrometry, indicating that their absence from the CH0210 plasma was not a technical artifact.
  • the light-chains belonging to these three clonotypes all shared the same V- and J- gene identity (IGKV1-39, IGKJ2) as the light-chains of the DH511 clonal lineage isolated by memory B cell single-cell sorting.
  • Six plasma mAbs belonging to the DH511 clonal lineage (designated DH511.7P-DH511.12P), showed potent tier 2 neutralizing activity against a panel of four HIV-1 isolates (Supplementary Table 7), with mAbs DH511.11P and DH511.12P demonstrating the most potent neutralizing activity.
  • DH511.11P and DH511.12P were selected for further characterization of their neutralization breadth and potency against a panel of 203 cross-clade isolates and had slightly more breadth (99.5% of isolates tested) and greater potency than memory B cell-derived DH511.2 but were less potent than 10E8 (median IC 50 : 0.7 ug ml for DH511.11P and DH511.12P versus 0.4 ug/ml for 10E8) (Supplementary Table 8).
  • both plasma derived variants recognized a conformation of the MPER similar to that recognized by DH511.1 and DH511.2, adopting an ⁇ -helix between residues 671-683 and an extended conformation upstream, between residues 662-670.
  • the highest degree of structural homology occurred between residues 668-683.
  • interactions between DH511.11P and DH511.12P and gp41 were mediated exclusively by their heavy chains (Fig. 60d and Supplementary Table 14).
  • the plasma-derived variants recognized the very same gp41 residues as those recognized in common by DH511.1 and DH511.2, although the respective antibody residues that mediated these contacts with gp41 differed in some cases (Fig.
  • DH511.1 IP and DH511.12P were highly homologous to those of DH511.1 and DH511.2.
  • the plasma- derived variants examined here recognized a similar conformation of the gp41 MPER as that recognized by memory B-cell derived variants, contacted a similar set of gp41 residues, and did so through modified antibody contacts that did not significantly alter the backbone conformations of their paratopes or common epitope.
  • V H 3-15-encoded gp41- contacting residues in DH511.1, DH511.2 and 10E8 we compared V H 3-15-encoded gp41- contacting residues in DH511.1, DH511.2 and 10E8.
  • V H 3-15-encoded gp41- contacting residues in DH511.1, DH511.2 and 10E8 Of the total number of residue interactions that exist between the V H 3-15 regions of three respective antibodies and gp41 (8 for DH511.1, 10 for DH511.2, and 10 for 10E8), five common residue positions were involved interactions with gp41 in all three antibodies: 28, 31, and 33 within the HCDRl and 52c and 53 within the HCDR2 (Fig. 61c and 60e).
  • Heavy chain residues 31 and 33 are asparagine and tryptophan in all three antibodies and are un-mutated from the germ-line precursor.
  • Residue 53 is aspartate in DH511.1 and DH511.2, as it is in the germ-line precursor, and a chemically similar glutamate in 10E8.
  • Residue positions 28 and 52c are somatically mutated from germ-line in all three antibodies, to disparate amino acids (Fig. 61e). While all five residues maintain contact with gp41 in both the DH511.1 and 10E8 lineages, the rotational shift in the orientations of the heavy and light chains between the two lineages results in distinct modes of gp41 recognition (Fig. 60b and 61e).
  • V H 3-15 encoded gp41 -contacting residues in both lineages end up interacting with many of the same gp41 MPER residues, including L669, W670, N671, W672, and F673 (Fig. 60b, 60e, and 61e).
  • V H 3-15 germ line encoded residue W33 shown in previous studies to be required for 10E8 recognition of gp41 (1), interacts with gp41 residues W672 and F673 in both the DH511.1 and 10E8 lineages, although from a distinct spatial position in each case (Fig. 60b and 61e).
  • a maximum likelihood phylogenetic tree was constructed from the VDJ sequences recovered from memory B cell sorting and was used to infer the unmutated common ancestor (UCA) of clone DH511 and six maturational intermediate antibodies (Fig. 59b).
  • UCA unmutated common ancestor
  • Fig. 59b six maturational intermediate antibodies
  • a global panel of 12 HIV-1 isolates was used to assess the development of neutralization breadth in the DH511 clonal lineage. None of the isolates were neutralized by the UCA or intermediate (I) 6 antibody that was most closely related to the DH511 UCA. Antibody 12 and later members of the lineage acquired the ability to neutralize 12/12 isolates (Supplementary Table 19).
  • DH511 clone acquisition of breadth was associated with the accumulation of somatic mutations, but neutralization potency did not directly correlate with percent V H mutation frequency.
  • Analysis of a panel of MPER peptides and MPER peptide liposomes did not reveal constructs that bound to the UCA. Binding to the MPER peptides was acquired at the 15 stage of maturation ( Figures 66 and 67).
  • DH511 inferred UCA and intermediates 11-13 and 16 reacted with several autoantigens as measured by ELISA ( Figures 68-69) and were found to exhibit polyreactivity in a protein microarray against 9,400 human proteins (3) ( Figure 68).
  • the mature members of the lineage were not polyreactive by ELISA, although some members demonstrated polyreactivity by microarray analysis (DH51 1.1, DH51 1.5, DH51 1.6, and DH51 1.12P). All DH51 1 lineage members lacked reactivity by indirect immunofluorescence human epithelial (HEp-2) cell staining assay.
  • HEp-2 indirect immunofluorescence human epithelial
  • mature bnAb DH51 1.2 reacted with the E3 ubiquitin ligase STIP1 Homology and U-Box Containing Protein 1 (STUB 1) while both DH51 1.1 1P and DH51 1.12P reacted with nuclear distribution gene C homolog (A. nidulans) (NUDC); DH51 1.12 also reacted with Scm-like with four MBT domains protein 1 (SFMBT1) ( Figure 68).
  • lipid reactivity of the DH51 1 clonal lineage we first determined propensity for lipid membrane binding/insertion of DH51 1.1-DH51 1.6 based on HCDR3 hydrophobicity. Three or more Phe or Trp amino acid residues were contained within the HCDR3 sequences of each DH51 1 clonal lineage member, and several members were found to have at least one Pro, with the exception of DH51 1.3 and DH51 1.6.
  • a membrane insertion score was calculated based on the Wimley-White hydrophobicity scale, which measures the propensity of amino acids to sit at the interface of the head and tail group in a lipid bilayer. Notably, membrane insertion scores were similar between the most potent neutralizer DH51 1.2 and 4E10/10E8 but differed from 2F5 (Supplementary Table 21).
  • DH511.2 K3 (comprised of the DH511.2 heavy-chain reconstituted with the plasma light- chain of DH511.8P), showed greater potency than 10E8 (Supplementary Table 24).
  • DH511.2 K3 neutralization data are shown in Figure 28 and 58.
  • HIV-1 antibody responses In the case of HIV-1 antibody responses, the relationship of the memory B cell and plasma antibody pools is complicated by the damage that HIV-1 inflicts on the B cell lineage with disruption of the germinal center in the earliest stages of infection (31), and the accumulation of FcRL4+ memory B cells in chronic infection (8). Interestingly, HIV-1- specific B cell responses are enriched in the FcRL4+ memory B cell compartment and exhibit many features of premature exhaustion (8). Regarding antibodies that target the Env bnAb epitope at the CD4 binding site, it has been shown that -60% of this response is contained within the exhausted FcRL4+ memory B cell compartment, thus preventing their progression to plasma cells and production of secreted antibody (8, 9).
  • HIV-1 infected individuals can make productive, albeit subdominant, bnAb responses that progress to plasma cell differentiation and secretion into blood plasma.
  • a critical question is whether memory B cells in HIV-1 infected individuals are differentiating into the long-lived plasma cell pool that resides in bone marrow and is responsible for long-lived plasma antibody responses (41).
  • the half-life of influenza antibodies did not decay over the time studied (42).
  • references [0287] 1. Huang J, Ofek G, Laub L, Louder MK, Doria-Rose NA, Longo NS, Imamichi H, Bailer RT, Chakrabarti B, Sharma SK, Alam SM, Wang T, Yang Y, Zhang B, Migueles SA, Wyatt R, Haynes BF, Kwong PD, Mascola JR, Connors M. 2012. Broad and potent neutralization of HIV-1 by a gp41-specific human antibody. Nature 491 :406-412.
  • HIV-1 envelope induces memory B cell responses that correlate with plasma antibody levels after envelope gpl20 protein vaccination or HIV-1 infection. Journal of immunology 183 :2708-2717.
  • Plasma and peripheral blood mononuclear cells were collected from South African donor CH0210, chronically infected with a clade C virus for an unknown period at the time of enrollment in the Center for HIV/ AIDS Vaccine Immunology (CHAVI) 001 chronic HIV- 1 infection cohort (previously described in (33). Informed consent was obtained under clinical protocols approved by the Institutional Review Board of the Duke University Health System and clinical site in South Africa. The DH511 bnAb lineage was isolated from PBMC and plasma collected at 8 weeks post-study enrollment, where the viral load was 5, 180 copies/ml and CD4 T cell count was unknown, at which time donor CH0210 had not initiated anti-retroviral therapy (ART).
  • ART anti-retroviral therapy
  • Donor CH0210 plasma was screened for neutralization breadth utilizing standard experimental mapping and computational methods for epitope prediction (13, 43).
  • Anti- MPER bnAb activity was detected using two different assays: plasma neutralization of the HIV-2/HIV-1 MPER chimeric pseudovirus CIC and plasma adsorption with MPER peptide coated magnetic beads, followed by testing of adsorbed plasmas for reduction of neutralization activity as described previously (44).
  • An algorithm for Neutralization-based Epitope Prediction (NEP) (13, 43) was used to delineate the specificities mediating breadth against a panel of 21 diverse HIV-1 strains. The resulting linear coefficients on a scale of (0 to 1) from the computational procedure was used to predict the relative prevalence of each of the reference antibody specificities in donor CH0210 plasma.
  • KKKNEQELLELDKWASLWNWFDITNWLWYIRKKK-biotin conjugated to fluorophore-labeled streptavidins, yielding a tetramer with four MPER epitopes for surface Ig cross-linking.
  • Aqua blue vital dye (Invitrogen, Carlsbad, CA) was used to stain dead cells.
  • MPR.03 double positive CD16-CD14-CD3-CD235-CD19+IgD-CD38hi memory B cells were single cell sorted into individual wells of a 96-well plate containing reverse transcription (RT) reaction buffer (5 ⁇ _, of 5' first-strand cDNA buffer, 0.5 uL of RNaseOUT [Invitrogen, Carlsbad, CA], 1.25 ⁇ L ⁇ of dithiothreitol, 0.0625 uL Igepal CA-630 [Sigma, St.
  • RT reverse transcription
  • Immunoglobulin genes were amplified from RNA of isolated cells by reverse transcription- polymerase chain reaction (RT-PCR).
  • RT-PCR reverse transcription- polymerase chain reaction
  • 10 mM dNTPs New England Biolabs, Ipswich, MA
  • 3 ⁇ random hexamers at 150 ng/ml GeneLink, Hawthorne, NY
  • 1 ⁇ Superscript ® III Invitrogen, Carlsbad, CA
  • IgH, IgK, and Igk variable region genes were separately amplified from the cDNA by nested PCR, using AmpliTaq Gold ® 360 Mastermix (Invitrogen, Carlsbad, CA), heavy-chain (45) and light-chain gene-specific primers as previously described (46). PCR amplicons were purified and sequenced, and VHDJ h and VLJL genes, mutation frequencies, and CDR3 lengths were determined using the Clonanalyst software (47). Clonal relatedness and inference of the unmutated common ancestor (UCA) and intermediate antibodies were determined by computational methods as described in (26, 40, 48).
  • UCA unmutated common ancestor
  • antibody variable heavy-chain and light-chain genes were de novo synthesized (GenScript, Township, NJ), cloned into pcDNA3.1 expression vectors containing the constant regions of IgGl (46), and co-transfected at equal ratios in Expi 293i cells using ExpiFectamine 293 transfection reagents (Thermo Fischer Scientific, Waltham, MA) according to the manufacturer's instructions. Culture supematants were harvested and concentrated after 4-5 days incubation at 37°C and 8% C0 2 , followed by affinity purification by protein A column (Pierce, Thermo Fisher Scientific, Waltham, MA). Antibody purity was evaluated by SDS-Page and Coomassie Blue staining for heavy and light-chains of the appropriate size.
  • Binding of transiently transfected supematants and mAbs to HIV-1 Env proteins and peptides was detected by enzyme-linked immunosorbent assay (ELISA).
  • ELISA enzyme-linked immunosorbent assay
  • High-binding 384- well plates (Corning, Oneonta, NY) were coated overnight at 4°C or for 2 hours at room temperature with 2 ⁇ g/ml HIV-1 protein or streptavidin (for detection of binding to biotinylated peptides) in 0.1 M sodium bicarbonate (Sigma Aldrich, St. Louis, MO).
  • Horseradish peroxidase-conjugated goat anti-human IgG Fc antibody (Jackson ImmunoRe search Laboratories, West Grove, PA) was added to each well and incubated for 1 hour, after which plates were washed with PBS/0.1% Tween 20 and developed with SureBlue Reserve TMB One Component Microwell Peroxidase Substrate for 15 minutes (KPL, Gaithersburg, MD). Development was stopped with 0.1 M HC1, and plates were read at 450 nm. Experiments were performed in duplicate, and results were reported as logarithm area under the curve (Log AUC). For epitope mapping, purified mAbs were screened as listed above against a panel of MPR.03 alanine scanned peptides. Epitope positions were defined by MPR.03 alanine scan mutations that reduced the Log AUC by >50% compared to the wild-type peptide.
  • Neutralization assays were performed using HIV-1 Env pseudoviruses to infect TZM- bl cells as previously described (50, 51). A five-parameter hill slope equation was used to fit neutralization curves by non-linear regression and for determination of maximum percent inhibition (MPI) values. Titers were calculated as 50% or 80% inhibitory concentrations (IC 50 and ICso) and reported as the concentration of antibody causing a 50% or 80% reduction in relative luminescence units compared to virus control wells. Mapping of the MPER residues critical for neutralization was performed using a panel of alanine scanned COT6.15 Env pseudoviruses as described previously (20, 21).
  • Antibody binding to a panel of nine autoantigens including Sjogren's syndrome antigen (SSA), SSB, Smith antigen (Sm), ribonucleoprotein (RNP), scleroderma 70 (Scl-70), Jo-1, double-stranded DNA (dsDNA), centromere B (Cent B), and histone, was quantified by ELISA.
  • Anti-cardiolipin reactivity was measured using the QUANTA Lite ACA IgG III ELISA kit (Nova Diagnostics, San Diego, CA) per the manufacturer's instructions as previously described (52).
  • Antibodies were assayed for reactivity to the human epithelial cell line (HEp-2) by indirect immunofluorescence staining using the IFA ANA/Hep-2 Test System (Zeus Scientific, Somerville, NJ) per the manufacturer's protocol. Antibodies were diluted to 50 ⁇ g/ml and 25 ⁇ g/ml and scored negative or positive (1+ to 4+) at each dilution. Antibodies were also screened for binding to a panel of >9,400 human proteins using a Protoarray microarray (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions and as described in (6).
  • HEp-2 human epithelial cell line
  • the array was blocked and incubated on ice with 2 ⁇ g/ml HIV-1 antibody or the isotype control antibody, human myeloma protein, 15 IK (Southern Biotech, Birmingham, AL) for 90 minutes.
  • Antibody binding was detected with 1 ⁇ g/ml anti-human IgG-Alexa-647 secondary antibody (Invitrogen).
  • Arrays were scanned using a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA) at a wavelength of 635 nm, 10 ⁇ resolution, using 100% power and 650 gain.
  • the fluorescence intensity of antibody binding was measured with the GenePix Pro 5.0 program (Molecular Devices, Sunnyvale, CA).
  • DH511.2 neutralization was determined using a post-attachment HIV-1 pseudotyped virus neutralization assay described previously (53). Inhibitory concentrations of DH511.2, 10E8, and 4E10 mAb were added to TZM-bl cells incubated with B.BG1168 virus at different time intervals after infection. Infectivity was measured in relative light units (RLUs).
  • the cells were diluted with 10 mL of cold MACS buffer (PBS supplemented with 0.5% BSA and 2 mM EDTA), collected by centrifugation (300 g for 10 min at 4°C), and depleted of non-B cells using the Human Memory B Cell Isolation Kit with an LD column (Miltenyi Biotec) as per the manufacturer' s instructions. This yielded 400,000 - 500,000 B cells per vial.
  • cold MACS buffer PBS supplemented with 0.5% BSA and 2 mM EDTA
  • Oligo d(T) 25 magnetic beads (1 ⁇ diameter at a concentration of 45 ⁇ ⁇ beads/mL solution; NEB) were washed, subjected to focused ultrasonication (Covaris) to dissociate any aggregates, resuspended in 6 mL of lysis buffer (100 mM Tris-HCl pH 7.5, 500 mM LiCl, 10 mM EDTA, 1% Lithium dodecyl sulfate (LiDS), 5 mM DTT), and passed through the middle tube at a rate of 0.5 mL/min.
  • lysis buffer 100 mM Tris-HCl pH 7.5, 500 mM LiCl, 10 mM EDTA, 1% Lithium dodecyl sulfate (LiDS), 5 mM DTT
  • the outer tubing contained an oil phase (mineral oil containing 4.5% Span-80, 0.4% Tween-80, and 0.05% Triton X-100; Sigma-Aldrich) flowing at 3 mL/min.
  • the cells, beads, and lysis buffer were emulsified as they passed through a custom designed 120 ⁇ diameter orifice, and were subsequently collected in 2 mL microcentrifuge tubes. Each tube was inverted several times, incubated at 20°C for 3 minutes, and then placed on ice. Following the collection phase, emulsions were pooled into 50 mL corneals, and centrifuged (4,000 g for 5 min at 4°C).
  • the mineral oil (upper phase) was decanted, and the emulsions (bottom phase) were broken with water- saturated cold diethyl ether (Fischer). Magnetic beads were recovered following a second centrifugation step (4,000 g for 5 min at 4°C) and resuspended in 1 mL of cold Buffer 1 (100 mM Tris pH 7.5, 500 mM LiCl, 10 mM EDTA, 1% LiDS, 5 mM DTT).
  • cold Buffer 1 100 mM Tris pH 7.5, 500 mM LiCl, 10 mM EDTA, 1% LiDS, 5 mM DTT.
  • the beads were then serially pelleted using a magnetic rack, and washed with the following buffers: 1 mL lysis buffer, 1 mL Buffer 1, and 0.5 mL Buffer 2 (20 mM Tris pH 7.5, 50 mM KC1, 3 mM MgCl).
  • the beads were split into two aliquots, and each was then pelleted one final time and resuspended in an RT-PCR mixture (19) containing VH and VL Framework Region 1 (FR1) linkage primers or VH and VL leader peptide (LP) linkage primers (Supplementary Tables 28 and 29).
  • FR1 VH and VL Framework Region 1
  • LP VH and VL leader peptide
  • RT-PCR mixtures were then added dropwise to 9 mL of chilled oil phase in an IKA dispersing tube (DT-20, VWR) and emulsified using an emulsion dispersing apparatus (Ultra- Turrax® Tube Drive; IKA) for 5 min.
  • IKA dispersing apparatus Ultra- Turrax® Tube Drive; IKA
  • the emulsions were aliquoted into 96-well PCR plates (100 uL/well), and subjected to RT-PCR under the following conditions: 30 min at 55°C followed by 2 min at 94°C; 4 cycles of 94°C for 30 s, 50°C for 30 s, 72°C for 2 min; 4 cycles of 94°C for 30 s, 55°C for 30 s, 72°C for 2 min; 32 cycles of 94°C for 30 s, 60°C for 30 s, 72°C for 2 min; 72°C for 7 min; held at 4°C.
  • the emulsions were collected in 2 mL microcentrifuge tubes and centrifuged (16000 g for 10 min at 20°C).
  • the mineral oil (upper phase) was decanted, and water- saturated ether was used to break the emulsions.
  • the aqueous phase (containing the DNA) was extracted three times by sequentially adding ether, centrifuging the samples (16000 g for 30 s at 20°C), and removing the upper ether phase. Trace amounts of ether were removed using a SpeedVac for 30 min at 20°C.
  • the DNA amplicons were purified using a silica spin column (Zymo-SpinTM I, Zymo Research) according to the manufacturer's instructions, and eluted in 40 ⁇ ⁇ H 2 0.
  • the two samples were then amplified through a nested PCR (see Supplementary Table 30 for primers) using Platinum Taq (Life Technologies) under the following conditions: (FR1 primer derived sample) 2 min at 94°C, 32 cycles of 94°C for 30 s, 62°C for 30 s, 72°C for 20 s; 72°C for 7 min; held at 4°C; (LP primer derived sample) 2 min at 94°C, 27 cycles of 94°C for 30 s, 62°C for 30 s, 72°C for 20 s; 72°C for 7 min; held at 4°C.
  • the amplicons approximately 850 bp in length, were gel purified from 1% agarose using a gel extraction kit (Zymo Research) according to the manufacturer'
  • the paired amplicon was subjected to an additional PCR using NEBNext high fidelity polymerase (NEB) to specifically amplify the full VH chain and the full VL chain separately in addition to the paired chains (Note: the paired reads sequence the entire J- and D-regions, and the fragment of the V regions spanning FR2 to CDR3).
  • NEB NEBNext high fidelity polymerase
  • protein samples were concentrated and resuspended in 50% (v/v) TFE, 50 mM H 4 HCO 3 and 2.5 mM DTT and incubated at 55°C for 45 min. The reduced samples were then alkylated with IAM in the dark, at room temperature for 30 min. The reaction was quenched by addition of DTT and the samples were diluted to 5% TFE and digested with trypsin (trypsin/protein ration of 1 :75 at 37°C for 5 h). The digestion was stopped by addition of formic acid to 1% (v/v).
  • the resulting PSMs were filtered with Percolator (Proteome Discoverer 1.4) to control false discovery rates (FDR) to ⁇ 1% and the average mass deviation (AMD) was calculated for all high-confidence PSMs and peptides with an AMD of ⁇ 1.5 ppm were kept for the final dataset.
  • Informative peptides, as defined previously (15), were grouped by their CDRHl, 2 or 3 association and for each group the abundances of the corresponding clonotypes were determined by the sum of the extracted-ion chromatograms of the respective precursor ions.
  • DH51 1.1 and DH511.2 fragments of antigen binding were set up in crystallization trials in complex with a panel of gp41 MPER peptides.
  • 576 initial conditions from commercially available screens were set up as vapor diffusion sitting drops robotically (TTP Labtech).
  • Crystals of DH511 Fab in complex with gp41 MPER peptide 656-683 were obtained in a condition composed of 30% PEG 1500, while those of DH511.2 Fab in complex with peptides MPR.03.DN4 and MPR.03.DN14, were obtained in 30% PEG 1500, 10% Isopropanol, 0.1 M CaCl 2 , 0.1 M Imidazole pH 6.5 and in 20% PEG 8000, 10% PEG 400, 0.5 M NaCl, 0.1 M C 2 H 3 Na0 2 pH 5.5, respectively. Crystal hits were hand optimized and X-ray diffraction data extended to 2.8, 2.65, and 2.2 A, respectively.
  • HIV-1 envelope induces memory B cell responses that correlate with plasma antibody levels after envelope gpl20 protein vaccination or HIV-1 infection. Journal of immunology 183 :2708-2717.

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Abstract

La présente invention concerne des anticorps neutralisant le VIH-1 et des procédés d'utilisation correspondants.
PCT/US2016/023488 2015-03-19 2016-03-21 Anticorps neutralisant le vih-1 et leurs utilisations WO2016149710A2 (fr)

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WO2021011544A1 (fr) 2019-07-16 2021-01-21 Gilead Sciences, Inc. Vaccins contre le vih et leurs procédés de fabrication et d'utilisation
WO2021130638A1 (fr) 2019-12-24 2021-07-01 Carna Biosciences, Inc. Composés modulant la diacylglycérol kinase
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